The invention discloses a method and system for calibrating an average protector response function of photovoltaic conversion modules. A lattice model is installed at the front end of a Gamma camera. The method comprises the steps: the Gamma camera works under the exposure condition of a pan-field radioactive source so as to output projected images and Gamma photon table mode data, and a digitization value of the output signal amplitude of each photovoltaic conversion module is obtained according to the table mode data; the projected images are divided to obtain the response position of incident Gamma photons in a Gamma detector in each segmentation area; an average value and variance of the signal amplitudes output by the Gamma photons, corresponding to each photovoltaic conversion module, entering different hole positions of the lattice model and deposited with all energy, and an average protector response function value at any position in a scintillation crystal plane is obtained according to the average value; the statistical characteristic of the output signal of each photovoltaic conversion module is obtained according to the average value and variance. By means of the method, operation is simple, convenient and quick, and the working amount in the data acquisition process is reduced.