To investigate the feasibility of label-free imaging using flat-field quantitative phase microscopy for observing mitochondrial dynamics in mesenchymal stem cells (MSCs) derived from bone marrow, SD rat bone marrow MSCs were isolated and cultured. Following passages and purification, they were seeded into confocal culture dishes and placed under a flat-field quantitative phase microscope developed by our team. Label-free observations were conducted over an extended period after confirming mitochondrial characteristics using fluorescence and phase dual channels. The mitochondrial division, fusion processes, and mitochondrial changes during cell apoptosis observed using the flat-field quantitative phase microscope were analyzed. The mitochondria observed via unlabeled flat-field quantitative phase microscopy exhibited complete overlap with fluorescently labeled mitochondria, demonstrating the microscope's capability to visualize mitochondria and conduct unlabeled high-resolution imaging. Moreover, the flat-field quantitative phase microscope facilitated long-term unlabeled observations of bone marrow MSCs under cultivation conditions, enabling high-resolution recording of mitochondrial division and fusion processes. Furthermore, we used the flat-field quantitative phase microscope to record mitochondria changes under CCCP treatment for the first time, visually presenting the apoptosis via mitochondrial pathway. The flat-field quantitative phase microscope allows for prolonged, unlabeled, high-resolution observations of cultured cells, offering a new tool for investigating mitochondrial dynamics.