Land surface temperature (LST) has a wide application in Earth Science-related fields, and spatial downscaling is an important method to retrieve high-resolution LST data. However, existing LST downscaling methods have difficulties in simultaneously constructing and expressing spatial non-stationarity, spatial autocorrelation, and complex non-linearity during the LST downscaling process, which limits the performance of the models. Moreover, there is a lack of research on high-resolution nighttime land surface temperature (NLST) reconstruction based on spatial downscaling, which does not meet the data needs for urban-scale nighttime urban heat island (UHI) studies. Therefore, this study combined Geographically Neural Network Weighted Regression (GNNWR) with Area-to-Point Kriging interpolation (ATPK) to propose a Geographically Neural Network Weighted Regression Kriging (GNNWRK) model for NLST downscaling. To verify the model’s generality and robustness, this study selected four study areas with different landform and climate type for NLST spatial downscaling experiments. The GNNWRK was compared with four benchmark downscaling methods, including TsHARP, Random Forest, Geographically Weighted Regression, and GNNWR. The results show that compared to these four benchmark methods, the GNNWRK method has higher accuracy in NLST downscaling, with a maximum Pearson’s Correlation Coefficient (Pcc) of 0.930 and a minimum Root Mean Square Error (RMSE) of 0.886 K. Moreover, the validation based on MODIS NLST data and ground-measured NLST data also indicates that the GNNWRK model can obtain more accurate, high-resolution NLST with richer and more detailed texture. This enhances the potential of NLST in studying the effects of urban nighttime heat islands at a finer scale.