Background: Presently, it is still lack of evidence whether a mechanical prosthesis is superior or inferior to a biological prosthesis in patients with Ebstein’s anomaly. The aim of this study was to compare the long-term results of mechanical and biological prostheses of patients with Ebstein’s anomaly at two major cardiac surgical centers in central China. Methods: From January 1999 to June 2020, 85 patients with Ebstein’s anomaly (mean age: 42 ± 17 years, male to female ratio = 19: 66) underwent tricuspid valve replacement. 22 patients (26%) underwent mechanical valve implantation, and 63 (74%) were implanted with a bioprosthesis. Median follow-up duration was 145 months and mean follow-up duration was 146 ± 13 months. Operative results, long-term survival, and tricuspid valve-related events were compared. Results: Eight patients suffered from cardiac failure and died within 30 days after the surgery. Mechanical prostheses demonstrated a better survival outcome compared with biological prostheses before (p = 0.043) and after (p = 0.039) propensity score matching. Tricuspid valve-related events occurred in 20 patients. There was no statistical significance between mechanical and biological tricuspid valves before (p = 0.87) and after (p = 0.91) propensity score matching. Conclusions: Tricuspid valve replacement for patients with Ebstein’s anomaly is a high-risk operation and should be cautious, especially for patients with poor conditions. Although mechanical prostheses demonstrated a better survival outcome compared with biological prostheses in our study, the selection of prostheses should be individualized and consider each patient’s characteristics and needs.