To investigate the differences in target volumes and dosimetric parameters between the supine and prone positions for external-beam partial breast irradiation (EB-PBI) after breast-conserving surgery (BCS) for Chinese breast cancer patients, thirty breast cancer patients who underwent three-dimensional conformal radiation therapy (3DCRT) EB-PBI after BCS were enrolled. Supine and prone scan sets were acquired during free breathing for all patients. Target volumes and organs at risk (OARs) including the heart, ipsilateral lung and bilateral breast were contoured by the same radiation oncologist. For each patient, supine and prone EB-PBI plans were generated based on the same planning criteria. The clinical target volume (CTV) and planning target volume (PTV) in the prone position were significantly greater than those in the supine position (P = 0.003, 0.004, respectively). A 0.95 Gy reduction in the mean dose (Dmean) to the heart (P = 0.000) was apparent in the supine position compared to the prone position. The Dmean to the ipsilateral lung was significantly lower in the prone position than in the supine position (1.59 Gy vs. 1.72 Gy, P = 0.029). Therefore, for Chinese breast cancer patients, carrying out 3DCRT EB-PBI in the prone position during free breathing is feasible.