To meet the demand of 3D real-time dose verification in radiotherapy, the 3D dose measurement technology based on scintillator luminescence was proposed. Based on the principle of scintillator luminescence by radiation, the 3D dose distribution was converted into 3D light distribution, and the 3D light distribution was measured and reconstructed by camera and optical emission tomography. The iterative algorithm was needed for 3D reconstruction based on optical emission computed tomography, and the system response matrix was an important parameter for iterative reconstruction. A calculation method of system response matrix based on point cloud distribution was proposed on the basis of pinhole imaging model, which converted voxels into random point clouds and calculated the number of point cloud projected in the pixels as the response of voxels to pixels. In the comparison of simulated imaging, compared with the traditional calculation method based on projection area, the proposed method suppressed the stripe-like error on the simulated images, improved the uniformity and gradient uniformity of simulated images, and improved the simulation accuracy, which was conducive to improving the accuracy of 3D reconstruction.