Fabrication of high performing CZTSSe absorber material from environmental benign nanocrystals ink is very important for large‐scale manufacturing production. Herein, the high‐quality metastable wurtzite Cu2ZnSnS4 (W‐CZTS) and wurtzite Cu2ZnSn(S1−x,Sex)4 (W‐CZTSSe) nanocrystals with small sizes have been synthesized successfully using dodecanethiol (DDT) and Se‐octadecylamine (Se‐ODA) as the sulfur and selenium sources, respectively. Compared to the thin film obtained from W‐CZTS nanocrystals ink, the thickness of small grain layer in the thin film obtained from W‐CZTSSe nanocrystals is reduced significantly. Further the ZnO nanoarrays (NAs)/CZTSSe heterojunction thin‐film grows on fluorine‐doped tin oxide (FTO) substrate and it exhibits superior photoelectrochemical (PEC) performance under light illumination. The ZnO NAs/CZTSSe heterojunction thin film shows the photocurrent density of 3.44 mA cm−2, which is nearly 2.7‐fold higher than the photocurrent density of ZnO NAs. The PEC efficiencies of ZnO NAs and ZnO NAs/CZTSSe are 0.4% and 1.89%, respectively. Our results demonstrate that the as‐synthesized W‐CZTSSe nanocrystals by using Se‐ODA are a promising precursor to fabricate high performing thin film, the Se‐ODA can be applied to prepare the precursors of chalcogenide thin film (including CISe, CIGSe, and CZTSSe).