Cu2ZnSnS4 (CZTS) nanocrystals with different morphologies and phases have been synthesized in hot organic solvents such as dodecanethiol and oleylamine. The crystallographic phases could be controlled by the sulfur precursor and the ligand species of the metal salts used for the synthesis. When a highly reactive sulfur precursor and metal acetates were used, wurtzite CZTS nanocrystals were obtained. On the other hand, using a low-reactivity sulfur precursor or metal chlorides produced CZTS nanocrystals in a kesterite phase. The experimental results from systematic investigations that the reaction rate between Zn and S precursors played a determining role for the growth of CZTS nanocrystals with different crystalline phases. A relatively faster reaction between Zn and S precursors in comparison to the Sn-S reaction favored the formation of a metastable wurtzite phase, which could be accelerated by increasing the reactivity of the S precursor. This work provided a safe and economical way to synthesize high-quality phase-controlled Cu2ZnSnS4 nanocrystals, especially wurtzite nanorods, for potential photovoltaic applications. Moreover, preliminary results show that the proposed mechanism also applies to the phase-controlled synthesis of other quaternary Cu2MSnS4 (M = Cd2+, Mn2+) nanocrystals.