The invention provides a missing marker filling method based on a sliding window sparse convolution denoising auto-encoder, which comprises the following steps: firstly, carrying out numerical conversion and one-hot coding on known gene data, dividing a training set and a verification set, then building a sparse convolution neural network model, carrying out missing marker filling on a gene sequence by adopting a segmented sliding window mode, and finally, obtaining a missing marker filling result; through overlapping of windows, central area prediction results with sufficient data features are obtained and spliced, and filling results of edge areas are abandoned. And then the filling precision of the missing mark is calculated, and the hyper-parameter of the neural network is adjusted according to the feedback result of the early-stage training. In practical application, gene filling results of multiple species such as corn and rice show that the filling precision of the method is remarkably higher than that of traditional algorithms such as KNN and SVD. The method is high in filling precision, has the advantages of simple model structure and high training efficiency, and has a wide application prospect in the field of gene sequence analysis.