It is always highly desirable to synthesize functional nanomaterials using cheap, naturally abundant clay deposits as starting materials, but the major challenge is lack of new way to utilize all of components in clay deposits and minimize the generation of waste. In order to resolve the problem, we proposed a “split” and “reconstruct” strategy to tailor palygorskite (Pal) clay deposits, and used each component to synthesizing three new nanomaterials with different morphologies and functions: copper silicate nanotube (CuSiO3), silica nanotube@Cu nanoparticles (SiO2-NT@Cu), and Mg-Al-Fe layered double hydroxide (LDH). The Pal clay deposits were first subjected to an acid bleaching process to obtain silica nanorods and solution rich in Mg(II), Al(II), Fe(III) ions. The silica as a Si source may react with Cu(II) to form CuSiO3 nanotube, which was allowed to be in-situ reduced in vapor or liquid phase to produce coral-like SiO2-NT@Cu nanocomposite with well-distributed Cu nanoparticles (CuNPs). The solution rich in Mg(II), Al(II), Fe(III) was used to synthesize Mg-Al-Fe LDH nanosheets by a simple co-precipitation process. It was confirmed that the tubular SiO2-NT@Cu nanocomposite can inhibit effectively the growth of E. coli and S. aureus, with the minimal inhibitory concentration (MIC) of 2.0 mg/mL and 0.6 mg/mL, respectively. The 2D nanolayered LDH compounds can capture efficiently and selectively anionic dye Congo Red (CR) with a maximum adsorption capacity of 254.14 ± 7.72 mg/g, due to an ion exchange and electrostatic attraction mechanism. This work provides a universal, cost-efficient and sustainable way to utilize all of components in low-grade natural clay deposits to synthesize useful nanomaterials with special functions, and also opens a new avenue for high-value utilization of abundant clay deposits.