Complete meteorological data is essential for meteorological research. However, due to sensor failure or occlusion, data loss always occurs. In order to deal with this problem, geoscience often uses Kriging and other traditional interpolation methods. Nevertheless, because the traditional method only considers the existing data, it cannot provide accurate reconstruction results when the spatial missing rate is large. Inspired by image inpainting algorithms, we propose a new deep learning method that combines other variables related to missing meteorological variables to provide more effective information for missing regions, and proves the good effect of the method through a series of experiments. To illustrate that our method can maintain good performance under different missing rates, we use the reanalysis data of the European Centre for Medium-Range Weather Forecasts to create a data set with three different missing rates of 30%, 50%, and 70% through the artificial mask. Under different missing rates, the average RMSE of the method based on deep learning decreased by 77% and 31% respectively compared with Kriging and DINEOF. In addition, by combining relevant variables, the accuracy of the deep learning model can be further improved by about 16%.