The thermal decomposition of Zn-MPA complex was investigated under microwave irradiation. ZnO and ZnS nanocrystals could be obtained by decomposing Zn-MPA(3-mercaptopropionic acid) complex under different reaction conditions. It was found that both the pH value of the solution and the molar ratio of Zn2+ and MPA can play an important role in the formation of ZnO and ZnS nanocrystals. MPA mainly acts as an S source or as a complexing agent.This study provides a new route for the controllable preparation of semiconductor nanocrystals.