In this paper, we analytically study the phase structure and construct the Ruppeiner geometry in the extended phase space for the five-dimensional neutral Gauss-Bonnet AdS black hole. Through calculating the scalar curvature of the Ruppeiner geometry and combining the phase transition, we show that the attractive interaction is dominant in the microstructure of the black hole system. More significantly, there is an intriguing property that the normalized scalar curvature has the same expression for the saturated small and large black hole curves. This implies that although the microstructure is different before and after the small-large black hole phase transition, the interaction between the microscopic constituents keeps unchanged. These results are quite valuable on further understanding the microstructure of the AdS black hole in modified gravity.