The invention relates to a modulating method and system for accurate dose distribution in the radiation therapy. According to the method, in the fractionated therapy positioning process, a 4D CBCT image of a patient is obtained, and a target region movement model is constructed in combination with a breathing movement signal; in the fractionated therapy process, the breathing movement signal and a non-autonomy movement signal of the patient are monitored in real time through an optical positioning system, with the help of the target region movement model, the movement position of a tumor is rapidly predicted, the positions of blades of a multi-blade collimator are adjusted in real time, and therefore ray bundles closely track the tumor for accurate therapy. In the whole therapy process, the patient freely breaths, an accelerator emits the bundles constantly, in this way, the therapy time is shortened, dose errors which are caused by the breathing movement and non-autonomy movement of the patient in the therapy are eliminated, and accuracy of the radiation therapy is improved.