Large-state cryptographic S-boxes can provide better obfuscation for symmetric encryption algorithms, but the costs for evaluating their properties are very expensive. To efficiently evaluate the differential properties of large-state cryptographic S-boxes, a GPU-based method for evaluating the differential properties of large-state cryptographic S-boxes was proposed. According to the existing differential uniformity calculation method, the GPU parallel schemes were designed for evaluating differential uniformity of 16-bit S-boxes and differential properties of 32-bit S-boxes respectively. The execution efficiencies of kernel functions and GPU were improved by the schemes, and the time costs were reduced by optimizing GPU parallel granularity and load balancing. The test results show that, compared with CPU methods and GPU parallel methods, the time costs of the proposed schemes for evaluating the differential properties of large-state cryptographic S-boxes are greatly reduced. The time for computing the differential uniformity of 16-bit S-box is 0.3 min; for a single input differential of 32-bit S-box, the time for computing the maximum output differential probability is about 5 min, and the time for evaluating the differential properties is about 2.6 h.