PURPOSE: To analyze the influence of the bladder and rectum filling and the body contour changes on the prostate target dose. METHODS: A total of 190 cone-beam CT (CBCT) image data sets from 16 patients with prostate cancer were used in this study. Dose reconstruction was performed on the virtual CT generated by the deformable planning CT. Then, the effects of the bladder filling, rectal filling, and the patient's body contour changes of the PCTV1 (the prostate area, B1) and PCTV2 (the seminal vesicle area, B2) on the target dose were analyzed. Correlation analysis was performed for the ratio of bladder and rectal volume variation and the variation of the bladder and rectal dose. RESULTS: The mean Dice coefficients of B1, B2, bladder, and rectum were 0.979, 0.975, 0.888 and 0.827, respectively, and the mean Hausdorff distances were 0.633, 1.505, 2.075, and 1.533, respectively. With the maximum volume variations of 142.04 ml for the bladder and 40.50 ml for the rectum, the changes of V100, V95, D2, and D98 were 1.739 ± 1.762 (%), 0.066 ± 0.169 (%), 0.562 ± 0.442 (%), and 0.496 ± 0.479 (%) in PCTV1 and 1.686 ± 1.051 (%), 0.240 ± 0.215 (%), 1.123 ± 0.925 (%), and 0.924 ± 0.662 (%) in PCTV2, respectively. With a 10% increase in the volume of the bladder and rectum, the V75, V70, and V65 of rectum increased at 0.73 (%), 0.71 (%), and 1.18 (%), and the V75, V70, and V65 of bladder changed at -0.21 (%), -0.32 (%), and -0.39 (%), respectively. CONCLUSION: Significant correlations were observed between the volume variation and the dose variation of the bladder and rectum. However, when a bladder and rectal filling protocol was adopted, the target dose coverage can be effectively ensured based on CBCT guidance to correct the prostate target position.