Practical applications of computed tomography (CT) in optical engines require an advanced algorithm that can correct the light refraction through optical windows and reconstruct the 3D signal field partially blocked by structural obstacles. In this work, an advanced CT algorithm is designed for optical engines to simultaneously eliminate the imaging distortion by refraction and to diminish the reconstruction error by partial signal blocking. By combining the pinhole model and Snell’s law, the ray-tracings from discretized 3D voxels in the measurement domain to 2D pixels on the imaging planes are accurately calculated, which restores the distortion on recorded projections. Besides, by deciding the locations and numbers of voxels that actually participate in iterative CT calculation, the iterative update process of voxel intensity becomes independent of the blocked rays, which reduces the reconstruction error. The algorithm is then numerically validated by reconstructing a simulated signal phantom inside an optical cylinder with a lightproof obstacle between the phantom and one recording camera, which imitates the refraction and blocking conditions in practical optical engines. Moreover, experimental demonstration is performed by reconstructing practical premixed flame inside optical engines. Both the simulation and the experiment present significantly enhanced flame chemiluminescence reconstruction by applying the optimized CT algorithm compared to the original algorithm utilized in open-space applications.