Abstract This paper describes a simple and efficient physics-based method for designing optimal transonic multistage compressor rotors. The key to this novel method is that the spanwise variation of the parameter which controls the three-dimensional shock structure, the area ratio between the throat and the inlet, “Athroat /Ainlet”, is extracted directly from the 3D computational fluid dynamics (CFD). The spanwise distribution of the area ratio is then adjusted iteratively to balance the shock structure across the blade span. Because of this, the blade design will be called “aerodynamically balanced.” The new design method converges in a few iterations and is physically intuitive because it accounts for the real changes in the 3D area ratio that directly controls the shock structure. Specifically, changes in both the spanwise 3D flow and the rotor’s operating condition; thus aiding designer understanding. To demonstrate this, two example design cases are shown in the paper: a transonic rotor within a multistage civil compressor with variable upstream stator vanes, and an embedded rotor within a multistage military fan. The method is shown to (1) improve both the operating range and the design efficiency while retaining the compressor’s overall matching, and (2) allow a balanced design to be simultaneously achieved at multiple shaft speeds. The result is a method which simplifies the multistage transonic compressor rotor design process and therefore has great practical utility.