Pre-stack seismic inversion of the P- and S-wave velocities and bulk density is important in seismic exploration for evaluating lithological units and fluid properties. Generally, this inversion is based on ray-tracing modeling, which introduces errors and requires substantial pre-processing for stratified models due to its oversimplified single-interface assumption. To overcome those problems, we propose a pre-stack inversion method, using wave-equation-based modeling as a forward engine. Most wave-equation-based pre-stack inversions are based on the reflectivity method and adopt nonlinear optimization algorithms, although accurate, but computationally expensive. Hence, we use a fast propagator matrix (PM) method valid for layered media. To improve the stability and accuracy, the PP data inversion is extended to joint PP and PS PM-based inversion (JPMI). A linear inversion scheme is adopted to reduce the computational cost, and the Frechet derivatives are computed accordingly. Moreover, to obtain an optimal model solution, the L-BFGS (Limited-memory Broyden–Fletcher–Goldfarb–Shanno) optimization algorithm and L-curve criterion, an adaptive regularization parameter acquisition method, are implemented. A posterior probability analysis shows that the method has a higher parameter sensitivity than the joint exact Zoeppritz-based inversion and gives better estimations than the single-data inversion. We discuss the effects of dataset weight, internal multi-reflections, time window setting, noise level and initial model by using model tests. Synthetic and real-data examples demonstrate that the algorithm is better than the single PP inversion in terms of stability and accuracy, especially for S-wave velocity and density estimations.