Recent studies in dynamic source modeling and kinematic source inversion show that earthquake rupture may contain greater complexity than we previously anticipated, including multiple slipping at a given point on a fault. Finite source inversion methods suffer from the nonuniqueness of solutions, and it may become more serious if we aim to resolve more complex rupture models. In this study, we perform synthetic inversion tests with dynamically generated complex rupture models, including both supershear rupture and slip reactivation, to understand the possibility of resolving complex rupture processes by inverting seismic waveform data. We adopt a linear source inversion method with multiple windows, allowing for slipping from the nucleation of rupture to the termination at all locations along a fault. We regularize the model space effectively in the Bayesian framework and perform multiple inversion tests by considering the effect of inaccurate Green’s functions and station distributions. We also perform a spectral stability analysis. Our results show that it may be possible to resolve both a supershear rupture front and reactivated secondary slipping using the linear inversion method if those complex features are well separated from the main rupture and produce a fair amount of seismic energy. It may be desirable to assume the full complexity of an earthquake rupture when we first develop finite source models after a major event occurs and then assume a simple rupture model for stability if the estimated models do not show a clear pattern of complex rupture processes.