Relative copy number of mitochondria was estimated for the potential association with the expression of mitochondrial coded stress related genes in bubaline spermatozoa. Semen samples were collected from buffalo bulls under two extreme temperature-humidity index conditions: hot summer and winter. Based on the semen quality, the bulls were categorized: exhibiting poor semen quality during hot summer as "seasonally affected," while those maintaining good semen quality throughout the year, as "seasonally not affected". The average mitochondrial copy numbers were lower during hot summer (15.42 ± 1.2368) compared to winter (17.29 ± 0.72) in both the groups. Furthermore, within the hot summer period, bulls classified as seasonally affected exhibited significantly lower mitochondrial copy numbers (12.86 ± 1.343) than their seasonally unaffected counterpart (17.97 ± 1.34). These results suggest a potential role of mitochondria in influencing semen quality, particularly in response to impaired scrotal thermoregulation during the summer season. Although the fold change in apoptotic genes (BCL2, MCL1, CASP3, and BAK) and oxidative panel genes (CAT, SOD, GPx, ATF4, and FOXO-3), did not differ significantly across the groups, differences were observed between the seasons. Further, to understand the role of copy number in apoptosis and ROS scavenging across the seasons and the groups, the generalized mixed model was employed. The results conveyed a significant negative interaction of copy number with the expression of CAT gene and significant positive interaction of copy number with the apoptotic gene panel. Our findings underscore the significant role of mitochondrial copy numbers in domestic buffalo spermatozoa in managing the challenges of thermoregulation posed by harsh tropical conditions.