Chondrosarcoma is characterized by the presence of histologically aggressive behavior, and commonly involves the scapula. Currently, limb salvage surgery is the recommended surgical treatment. Owing to the irregularity of the tumor, the suitability of an implant after tumor resection is a challenge for surgeons. Three-dimensional (3D) printing technology has the potential to make personalized limb salvage surgery a reality. We report the case of a 53-year-old man who was diagnosed with chondrosarcoma of the scapula. Considering the low-grade malignancy and lack of invasion of the glenoid, we agreed upon segmental scapula replacement as the treatment protocol. Nevertheless, reconstruction of the irregular bony defect remaining after tumor resection can be complicated. Therefore, a personalized prosthesis and navigation template corresponding to tumor was designed with 3D printing technique, and tumor resection, prosthesis implantation, and rotator cuff reconstruction were completed. The affected shoulder achieved satisfactory function during a 32-month follow-up with no tumor recurrence. 3D printing technique can help implement the individualized design of the implant and accurate reconstruction after tumor resection, simplify complicated operations, improve operational efficiency, and allow early functional recovery.