The spatial–temporal sampling errors arising from the differences in geographical locations and measurement times between co-located Global Navigation Satellite System (GNSS) radio occultation (RO) and radiosonde (RS) data represent systematic errors in the three-cornered hat (3CH) method. In this study, we propose a novel spatial–temporal sampling correction method to mitigate the sampling errors associated with both RO–RS and RS–model pairs. We analyze the 3CH processing chain with this new correction method in comparison to traditional approaches, utilizing Fengyun-3E (FY-3E) GNSS Occultation Sounder II (GNOS II) RO data, atmospheric models, and RS datasets from the Hailar and Xisha stations. Overall, the results demonstrate that the improved 3CH method performs better in terms of spatial–temporal sampling errors and the variances of atmospheric parameters, including refractivity, temperature, and specific humidity. Subsequently, we assess the error variances of the FY-3E GNOS II RO, RS and model atmospheric parameters in China, in particular the northern China and southern China regions, based on large ensemble datasets using the improved 3CH data processing chain. The results indicate that the FY-3E GNOS II BeiDou navigation satellite system (BDS) RO and Global Positioning System (GPS) RO show good consistency, with the average error variances of refractivity, temperature, and specific humidity being less than 1.12%2, 0.13%2, and 700%2, respectively. A comparison of the datasets from northern and southern China reveals that the error variances for refractivity are smaller in northern China, while temperature and specific humidity exhibit smaller error variances in southern China, which is attributable to the differing climatic conditions.