Multipath is the main systematic error of the Global Navigation Satellite System (GNSS) short baseline positioning. Multipath cannot be eliminated by the double-differenced technique and is difficult to parameterize, which severely restrict the high-precision GNSS positioning application. Based on the spatiotemporal repeatability of multipath, the sidereal filtering in coordinate-domain (SF-CD), the sidereal filtering in observation-domain (SF-OD), and the multipath hemispherical map (MHM) can be used to mitigate the multipath in real-time. However, the multipath model with large matrix for multi-GNSS multipath mitigation is difficult to achieve lightweight calculation and the SF-CD cannot be applied to mitigate the multi-GNSS multipath. In this paper, we propose a new multipath mitigation strategy in the coordinate-domain that shakes off the formation mechanism of multipath, a CNN (convolutional neural network)-LSTM (long short-term memory) method is used to mine the deep multipath features in GNSS coordinate series. Furthermore, multipath will be mitigated in real-time by constantly predicting the value of the next epoch. The experimental results show that the CNN-LSTM effectively mitigates the multi-GNSS multipath. The method can reduce the average RMS (root-mean square) of multi-GNSS positioning errors in the east, north, and vertical directions by 62.3%, 70.8%, and 66.0%. Moreover, comparing with the SF-CD, SF-OD, and MHM, CNN-LSTM can more effectively mitigate the effects of the GPS multipath, and the ability of multipath mitigation is almost not affected over time.