Substantial improvements in supersonic and hypersonic flight vehicles can be obtained by utilizing supersonic throughflow fans and compressors. However, the environmental impact of such future propulsion systems must be considered, such as their noise generation. In this regard, progress in engine noise control is dependent on developing an increased fundamental understanding of turbemachinery noise generation and on novel methods for controlling this noise which do not impose performance penalties on the engine. In this paper, a mathematical model is developed to analyze the effects of aerodynamic detuning on the discrete frequency noise generation of supersonic axial flow rotors, with the detuning achieved by alternating the circumferential spacing of adjacent rotor blades. This model is then applied to baseline uniformly spaced twelve bladed rotors and detuned configurations of these baseline rotors, with the effect of this aerodynamic detuning on the discrete frequency noise generation determined by considering the relative magnitudes of the gust generated unsteady aerodynamic lift. This study demonstrated that alternate blade circumferential spacing aerodynamic detuning is a viable passive discrete frequency noise generation control technique for supersonic throughflow rotors, depending on the specific blade row and flow field geometry.