In this study, we investigated the mitochondrial energy supply capacity and molecular mechanisms of apoptosis, mitochondrial fission, and mitophagy in regulating mitochondrial degeneration in testis of striped dwarf hamsters (Cricetulus barabensis) under mild low temperature (15°C) and short daylight (10 h:14 h) conditions. Results showed that under moderate daylight and mild low temperature (ML), short daylight and moderate temperature (SM), short daylight and mild low temperature (SL) conditions, the mitochondria were swollen and cristae were disrupted. Compared with the moderate daylight & moderate temperature group (MM; 12 h:12 h, 22°C), the number of mitochondria was significantly decreased in the SM and SL groups. Both short daylight and mild low temperature reduced the protein expression of citrate synthase, thus the energy supply capacity of mitochondria may be weakened. Compared with the MM group, bax/bcl2 protein expression was higher in three treatment groups, and caspase3 activity increased in SM and SL groups, suggesting that short daylight can induce apoptosis. DRP1 protein expression showed no difference in four groups, while the FIS1 protein expression was significantly decreased in three treatment groups, this indicates that short daylight and mild low temperature can increase mitochondrial fission level. PINK1 protein expression was significantly increased in ML and SL groups, indicates that mild low temperature will lead to increased mitophagy level. Generally, short daylight induced degeneration of mitochondria in the testis of hamsters mainly by increasing apoptosis, while under mild low temperature, balanced regulation of mitophagy and mitochondrial fission appear to contribute to the protection of mitochondria.