Due to the addition of confocal pinholes and the unstable output of terahertz laser currently, the performance of terahertz confocal scanning microscopic imaging is not high. The bilateral filtering algorithm is applied to the image denoising of transmission type terahertz confocal scanning microscopic imaging. Through the experiment, the bilateral filtering parameters are calculated to fit this situation. Moreover, through the comparison of the filtering performance with median filtering, average filtering and open operation filtering, it is proved that the bilateral filtering algorithm is feasible to apply for image denoising of transmission type terahertz confocal scanning microscopic imaging.