To compare two 3D graphs in Mathematica using the Plot3D command, users can create a new function representing the difference between the two original functions. This can be achieved by defining a new function, c, as the difference of the first function, a, and the second function, b (c = a - b). The Plot3D command can then be used to visualize this new function. The discussion includes a reference link to additional examples of using Plot3D for further guidance. This method allows for a clear comparison of the two graphs.