Purpose: The purpose of this study is to evaluate the effects of cone-beam computed tomography (CBCT) on dose distribution and normal tissue complication probability (NTCP) by constructing a comprehensive dose evaluation system for prostate intensity-modulated radiation therapy (IMRT). Methods: A system that could combine CBCT and treatment doses with MATLAB was constructed. Twenty patients treated with prostate IMRT were studied. A mean dose of 78 Gy was prescribed to the prostate region, excluding the rectal volume from the target volume, with margins of 4 mm to the dorsal side of the prostate and 7 mm to the entire circumference. CBCT and treatment doses were combined, and the dose distribution and the NTCP of the rectum and bladder were evaluated. Results: The radiation dose delivered to 2% and 98% of the target volume increased by 0.90 and 0.74 Gy on average, respectively, in the half-fan mode and on average 0.76 and 0.72 Gy, respectively, in the full-fan mode. The homogeneity index remained constant. The percent volume of the rectum and bladder irradiated at each dose increased slightly, with a maximum increase of <1%. The rectal NTCP increased by approximately 0.07% from 0.46% to 0.53% with the addition of a CBCT dose, while the maximum NTCP in the bladder was approximately 0.02%. Conclusions: This study demonstrated a method to evaluate a combined dose of CBCT and a treatment dose using the constructed system. The combined dose distribution revealed increases of <1% volume in the rectal and bladder doses and approximately 0.07% in the rectal NTCP.