Prunus sibirica is an economically important forest tree with great development prospects. To study the mechanisms of male sterile P. sibirica, we compared the phenotypic, cytological, and physiological characteristics of male sterile clone 1 with those of male fertile clone 60. Phenotypic characteristics of male sterile P. sibirica included abnormal anther dehiscence, short and unbent filaments, and distorted pollen. Cytological features of abnormal anther development in male sterile P. sibirica emerged following the late‐uninucleate stage and were characterized by delayed tapetum degeneration, delayed and limited secondary thickening of the endothecium, and incomplete mitotic division of pollen. Physiological traits of male sterile P. sibirica included excessive accumulation of reactive oxygen species (ROS) and low antioxidant enzyme activity. At the early‐binucleate stage, the content of malondialdehyde, superoxide radicals, and hydrogen peroxide in male sterile clone 1 was 2.48, 1.27, and 1.34 times of those in male fertile clone 60, respectively. At the late‐binucleate stage, superoxide dismutase in male sterile clone 1 was 50.48% of that in male fertile clone 60, and peroxidase activity in male sterile clone 1 was 36.62% of that in male fertile clone 60. In conclusion, we identified the characteristics and critical period of male sterility in P. sibirica, revealing the association between an imbalance in ROS homeostasis and male sterility.