Background and purposeThis study aims to explore the advantages and robustness of the partial arc combined with prone position planning technique for radiotherapy in rectal cancer patients. Adaptive radiotherapy is recalculated and accumulated on the synthesis CT (sCT) obtained by deformable image registration between planning CT and cone beam CT (CBCT). Full and partial volume modulation arc therapy (VMAT) with the prone position on gastrointestinal and urogenital toxicity, based on the probability of normal tissue complications (NTCP) model in rectal cancer patients were evaluated.Materials and methodsThirty-one patients were studied retrospectively. The contours of different structures were outlined in 155 CBCT images. First, full VMAT (F-VMAT) and partial VMAT (P-VMAT) planning techniques were designed and calculated using the same optimization constraints for each individual patient. The Acuros XB (AXB) algorithm was used in order to generate more realistic dose distributions and DVH, considering the air cavities. Second, the Velocity 4.0 software was used to fuse the planning CT and CBCT to obtain the sCT. Then, the AXB algorithm was used in the Eclipse 15.6 software to conduct re-calculation based on the sCT to obtain the corresponding dose. Furthermore, the NTCP model was used to analyze its radiobiological side effects on the bladder and the bowel bag.ResultsWith a CTV coverage of 98%, when compared with F-VMAT, P-VMAT with the prone position technique can effectively reduce the mean dose of the bladder and the bowel bag. The NTCP model showed that the P-VMAT combined with the prone planning technique resulted in a significantly lower complication probability of the bladder (1.88 ± 2.08 vs 1.62 ± 1.41,P= 0.041) and the bowel bag (1.28 ± 1.70 vs 0.95 ± 1.52,P< 0.001) than the F-VMAT. In terms of robustness, P-VMAT was more robust than F-VMAT, considering that less dose and NTCP variation was observed in the CTV, bladder and bowel bag.ConclusionThis study analyzed the advantages and robustness of the P-VMAT in the prone position from three aspects, based on the sCT fused by CBCT. Whether it is in regards to dosimetry, radiobiological effects or robustness, P-VMAT in the prone position has shown comparative advantages.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13014-023-02285-6.