The construction of the voxel model is an important part of computer ionospheric tomography (CIT) method. It will no doubt affect the accuracy of the CIT method. However, most existing researches focus on how to improve the image’s accuracy via inversion algorithm and few of them are concerned with the grid construction solution. This paper intends to improve accuracy by making some optimization on the voxel model. Some preliminary experiments were first carried out to explore the relationship between the accuracy of the image and its corresponding resolution. Then, based on the findings, a new CIT method, which is to improve the accuracy of the tomographic image of the interesting area at the price of reducing the resolution of the non-interesting area, was proposed. After that, some further experiments were taken to validate the new method. After comparing various accuracy indicators, such as root mean square error (RMSE), absolute mean error (MAE), 68% percentile, 95% percentile and stand deviation, the new method is showed to be better than the one that is not using the method proposed in this paper. According to our experiments, the new method is able to decrease RMSE/MAE of the tomographic image by 15% to 40%.