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Background: This study evaluated the feasibility, complications, graft survival rate, and clinical outcomes of joint-preserving resection using a custom-made endoprosthesis and liquid nitrogen-inactivated autologous bone graft reconstruction in patients with malignant bone tumors around the knee joint. Methods: We retrospectively analyzed 23 consecutive patients who underwent joint preservation surgery between 2008 and 2018 at our center. The study cohort included 13 patients who underwent custom-made endoprosthesis reconstruction and 10 who underwent liquid nitrogen-inactivated autologous bone graft reconstruction. The resected bone length, distance between the resection line and the joint, intraoperative blood loss, operation time, complications, and MSTS were compared between the two groups. Results: The median follow-up time was 68.5 months in the endoprosthesis group and 65.3 months in the inactivated autograft group. There were no significant differences in baseline characteristics, resected bone length, distance between the resection line and the joint, or intraoperative blood loss between the two groups. The operative time was longer in the inactivated bone graft group than in the endoprosthesis group (p < 0.001). The endoprosthesis group had more complications (six patients) and reoperations due to complications (five) than the inactivated autograft group (one), but there was no significant difference in the incidence of complications between the two groups (p = 0.158). The inactivated autograft group had one patient with type 1b complications, while the endoprosthesis group had one with type 1b complications, one with type 2b complications, and one with type 4a complications. One patient in the endoprosthesis group with type 5a complications experienced two soft tissue recurrences. The overall 5-year survival rate was 86.5% and the graft survival and final limb salvage rates were 100% in both groups. After the follow-up period, the mean MSTS scores were 91% ± 7% in the endoprosthesis group and 94% ± 6% in the inactivated autograft group, with no significant difference (p = 0.280). Conclusion: Joint-preserving resection is a reliable and effective tumor resection method that can achieve good postoperative function. There were no significant differences in the incidence of complications, overall survival rate, or graft survival rate between the two groups. [ABSTRACT FROM AUTHOR]