Unpredicted precipitations, even mild, may cause severe economic losses to many businesses. Precipitation nowcasting is hence significant for people to make correct decisions timely. For traditional methods, such as numerical weather prediction (NWP), the accuracy is limited because the smaller scale of strong convective weather must be smaller than the minimum scale that the model can capture. And it often requires a supercomputer. Furthermore, the optical flow method has been proved to be available for precipitation nowcasting. However, it is difficult to determine the model parameters because the two steps of tracking and extrapolation are separate. In contrast, current machine learning applications are based on well-selected full datasets, ignoring the fact that real datasets quite often contain missing data requiring extra consideration. In this paper, we used a real Hubei dataset in which a few radar echo data are missing and proposed a proper mechanism to deal with the situation. Furthermore, we proposed a novel mechanism for radar reflectivity data with single altitudes or cumulative altitudes using machine learning techniques. From the experimental results, we conclude that our method can predict future precipitation with a high accuracy when a few data are missing, and it outperforms the traditional optical flow method. In addition, our model can be used for various types of radar data with a type-specific feature extraction, which makes the method more flexible and suitable for most situations.