Developing advanced biocompatibility materials is of critical importance in biomedical engineering. Polyhydroxyalkanoates (PHA), being famous for its flexible mechanical properties, thermal properties, biocompatibility, and biodegradability, has been widely used in wound dressings, artificial blood vessels, heart valves, nerve conduits, bone and cartilage scaffolds, surgical sutures, and other fields. However, reports on the application of PHA in tissue repair and regeneration are often lacking in systematics. Here, a comprehensive and in-depth perception of the performance advantages and application value of PHA is provided. In this review, the following applications of PHA in biomedical engineering are covered: i) soft tissue, ii) organ tissue, iii) vascular tissue, iv) heart valve tissue, v) nerve conduit tissue, vi) bone tissue, vii) cartilage tissue and viii) others. Finally, an outlook on the future research directions and challenges of PHA is presented.