The invention discloses a brain nuclei Granger causal analysis method based on RYGB surgery weight losing. The method comprises the following steps of obtaining functional magnetic resonance data in a resting state scanning mode, preprocessing the data, carrying out regional homogeneity analysis on the preprocessed data, defining regions of interest according to the difference area of the brain of an obese patient one month before and after surgery, carrying out Granger causal analysis, selecting two areas from selected regions of interest at random, extracting time sequences of the two areas, calculating a Granger causal value between the two areas by adopting a first-order autoregressive model, and carrying out normalization, wherein the step of preprocessing the data comprises the steps of time rectification, head moving rectification and space standardization. According to brain nuclei Granger causal analysis method based on the RYGB surgery weight losing, the RYGB surgery weight losing changes the functions of brain reward loops, brain cognitive loops and brain drive loops and the mutual cause and effect relation among the loops, the crapulent degree of the obesity patient is relieved, and iconography proofs are provided for development of central nervous system medicine.