With green synthetic technology to avoid organic solvents, the aqueous medium is used to the dethiolation of 2-mercaptopyrimidine derivatives via the reduction activity of Raney-Ni. Specifically, the yield effect on the substitution, reaction solvents and temperature was optimized, along with the recycling possibility of Raney Ni and waster water. 4-Amino-6-hydroxypyrimidine, 4-aminopyrimidine, 5,6-diamino-4-hydroxypyrimidine and 4-hydroxypyrimidine were synthesized with the yields of 98%, 74%, 87% and 89%, respectively. The green synthetic process is stirred under reflux for 1-4 h, which can avoid organic solvents for improving the production safety.