Background: The choice between bioprosthetic and mechanical valves for aortic valve replacement (AVR) and mitral valve replacement (MVR) among patients aged 50–70 years is controversial. We compared the long-term outcomes of patients using bioprosthetic or mechanical valves to provide clinical evidence for valve selection. Methods: From 2002 to 2007, patients aged 50–70 years who underwent isolated AVR or MVR at the Fuwai Hospital were enrolled. After inverse probability-weighted (IPW) propensity balancing, we evaluated long-term mortality, stroke, and bleeding events between patients receiving mechanical and biological prostheses for MVR or AVR. Results: A total of 1639 patients were included in the study, including 1181 patients undergoing MVR (median follow-up: 11.6 years) and 458 patients undergoing AVR (median follow-up: 11.4 years). After IPW adjustment, there was no significant difference in long-term mortality and stroke rate between patients using bioprosthetic and mechanical valves for MVR [mortality: log-rank p = 0.802; stroke: log-rank p = 0.983] and AVR [mortality: log-rank p = 0.815; stroke: log-rank p = 0.537]. Landmark analysis at 12.5 years yielded significantly lower mortality in the patients receiving mechanical valves compared with bioprosthetic valves in the MVR cohort (p = 0.028). Patients receiving mechanical aortic valves displayed an increased risk of bleeding compared with those who received bioprosthetic aortic valves [Hazard Ratio (95% Confidence interval): 2.51 (1.06–5.93) p = 0.036]. Conclusions: For patients aged 50–70, there was no significant difference in overall long-term mortality between mechanical and bioprosthetic valve recipients. Patients receiving mechanical valves for MVR displayed lower mortality after 12.5 years follow-up. For AVR, bioprosthetic valves were associated with a lower risk of bleeding.