The accuracy of passive satellite cloud top height (CTH) retrieval shows regional dependence. This paper assesses the CTH derived from the FY-4A and Himawari-8 satellites through comparison with those from the ground-based millimeter radar at two sites: Yangbajing, Tibet, China (YBJ), and the Institute of Atmospheric Physics (IAP), Beijing, China. The comparison shows that Himawari-8 missed more CTHs at night than FY-4A, especially at YBJ. It is found that the CTH difference (CTHD; radar CTH minus satellite CTH) for FY-4A and Himawari-8 is 0.06 ± 1.90 km and −0.02 ± 2.40 km at YBJ respectively, and that is 0.93 ± 2.24 km and 0.99 ± 2.37 km at IAP respectively. The discrepancy between the satellites and radar at IAP is larger than that at YBJ. Both satellites show better performance for mid-level and low-level clouds than for high-level clouds at the two sites. The retrievals from FY-4A agree well with those from Himawari-8, with a mean difference of 0.08 km at YBJ and 0.06 km at IAP. It is found that the CTHD decreases as the cloud depth increases at both sites. However, the CTHD has no obvious dependence on cloud layers and fractions. Investigations show that aerosol concentration has little impact on the CTHD. For high and thin clouds, the CTHD increases gradually with the increase of the surface temperature, which might be a key factor causing the regional discrepancy between IAP and YBJ.