In this study, dexamethasone was used to induce mouse thymocyte apoptosis. The PI and Annexin V/PI staining flowcytometry methods were adopted to detect late and early phases apoptosis. Inner mitochondrial membrane potential (deltapsim) was examined by JC-1 and DiOC6(3)/PI staining flowcytometry. Direct JC-1 staining technology was applied to test the of deltapsim abstracted pure mitochondria. Results showed: DEX could significantly induce late and early phase mouse thymocyte apoptosis; at cell level, DEX was observed to reduce staining ability of deltapsim dependant fluorescence, J-aggregate and DiOC6(3), to drop down mitochondria number, but to cause no significant change of cell membrane integrity. Results of pure mitochondria detection showed most of them maintained normal deltapsim. According to above results, we concluded DEX could reduce mitochondria number when inducing mouse thymocyte apoptosis; and the remaining ones maintain normal function to meet the energy need for apoptotic process.