Organic dyes with intensive near-infrared (NIR) absorption have shown practical application for fluorescence imaging. Based on Diketopyrrolopyrrole (DPP) and Boron-dipyrromethene (BODIPY), NIR dyad BD and triad BDB with two BODIPY units have been synthesized. There is a great steric hindrance existing between the DPP and BODIPY units; however, triad BDB shows a little more effective intramolecular charge transfer than dyad BD, as result in a stronger absorbance of the longest absorption band. According to theoretical calculations, the longest absorption maxima are contributed by the HOMO-LUMO transition for both BD and BDB. Both dyes were then fabricated into hydrophilic nanoparticles (NPs) via nano-precipitation method, the NIR dyes and the corresponding NPs all exhibit excellent photostability. Furthermore, the NPs show great biocompatibility, low dark cytotoxicity on HeLa cells. While taking Zebrafish as the live-animal model, BD NPs and BDB NPs show good fluorescence imaging property.