Seed aging is a complex biological progress from quantitative change to qualitative change. Seed aging is closely related to the dysfunction of mitochondria. In the view of the “mitochondria aging theory”, the excessive accumulation of ROS in mitochondria is the main reason of seed aging. Understanding the changes takes place in mitochondria during seed aging is important to reveal the mechanism of seed aging and ensure safe conservation of seeds. In this paper, the current process of mitochondrial structure, respiration and antioxidant systems during seed aging were reviewed. Moreover, problems in the study of seed aging and mitochondria were discussed.