Surface plasmon resonance (SPR) effect of nanoparticles, is an emerging subfield of nanophontonics, and it attracts increasing attention because of its potential applications in controlling and manipulating light at nanoscale dimensions. This review focuses on the molecules mediated nanoparticle assemblies and their biological applications, highlights several molecules mediated nanoparticle assembly technique and their recent applications in biomedical, and prospects the future development. Based on the specific binding ability of these functional mediate molecules (including DNA, antigen-antibody, aptamar, biotin-avidin, small organic molecules and polymers), plasmonic nanoparticles could be synthesized by self-assemble methods. Noble metal nanoparticle assemblies have broad applications in biological sensing, imaging and treatment due to their exclusive plasmon optical properties. With the rapid development of self-assembly technology, molecule-mediated self-assembly technology can be used well to control the spatial arrangement structure of plasmonic nanoparticles. Individual nanoparticle has been used to controllable assembled into one-dimensional, two- dimensional or three-dimensional conformation of the novel composite materials. SPR effect of noble metal nanoparticles, is an emerging subfield of nanophontonics, and it attracts increasing attention because of its potential applications in controlling and manipulating light at nanoscale dimensions. Compared with the individual nanoparticle, nanoparticle assemblies have a lot of novel or excellent physical properties which exhibite convenient adjustable ability in SPR spectra due to noble metal nanoparticles with irregular shape. They show notable antenna effect at the edge of nanoparticles and the coupling effect between adjacent two nanoparticles. All of these unique optical properties on plasmonic nanoparticles will be further enhanced by the self-assemble nanotechnology, which exhibits many promising applications in the field of biosensors (including photocolorimetric method, SPR, surface-enhanced Raman scattering (SERS), circular dichroism etc.), photoacoustic imaging and photothermal therapy in recently decades. This review focuses on the molecules mediated nanoparticle assemblies and their biological applications, highlights several molecules mediated nanoparticle assembly technique and their recent applications in biomedical, and prospects the future development. Based on the specific binding ability of these functional mediate molecules (including DNA, antigen- antibody, aptamar, biotin-avidin, small organic molecules and polymers etc.) plasmonic nanoparticles clusters could be synthesized to molecules mediated nanoparticle assemblies (MMNAs) by self-assemble methods following the well-designed linker. MMNAs could be widely used in bionanotechnology and biomedicine. The MMNAs would exhibit more sensitivity to the imperceptible changes of micro-environment around the assembles. There would be larger shifts in this resonance due to changes in the local index of refraction upon adsorption to the nanoparticles which could be used to detect biopolymers such as DNA or proteins. For example, the satellite gold nanoparticles linked on the surface of core particle by DEVD peptide would be cleaned by caspase-3 from the core. This method has been used directly for real-time monitoring the enzymatic reaction by MMNAs’ scattering spectra shifts. In addition, there would be abundant hot-spots between the satellite nanoparticles and the core, which is emerging as a powerful tool for SERS spectroscopic detection of trace molecular, cellular, and in vivo targets. The enhancement factors could achieve up to 1014−1015 by properly adjusting the LSPR spectroscopic profile and structural features of the MMNAs. What’s interesting is that when noble metal nanoparticles aggregate, there has been a red-shift in the light absorption spectrum, which dramatically enhances the light absorbance in the NIR region. And the MMNAs would show great adjustable ability in plasmon resonance absorption which opening up new opportunities for plasmonic nanoparticles to be utilized as photosensitizers in the NIR photothermal therapy photoacoustic imaging applications. Based on the further comprehensive researches and developments of MMNAs in recent decades, we believe that the continued development of MMNAs will be applied well in the fields of chemistry, physics, optics and biomedicine in the future.