High yield mung bean powder goat milk cheese was optimized by the combination of single factor experiments and response surface methodology. A second-order rotation combination design was conducted using the content of starter, CaCl2, rennet, mung bean powder as the independent variables. And the protein structure of the mung bean powder goat milk cheese was studied by differential scanning calorimetry (DSC) and Fourier transform infrared (FTIR). Results indicated that the highest cheddar cheese yield of 9.640% was achieved when the extraction was carried out with mung bean powder of 0.900%, rennet 0.045%, CaCl2 0.035% and tarter of 1.000%, which was consistence with the model predicted value. DSC and FTIR of mung bean powder goat milk cheese tests showed that moderate protein hydrolysis mung bean powder goat milk cheese has a higher yield and a good thermal stability.