As an important topic of artificial intelligence, knowledge graphs have a wide range of applications such as semantic search, intelligent question answering, and visual decision support. Among them, the genealogy knowledge graph, as a kind of domain knowledge graph, has important application value in genetic disease analysis, population behavior analysis, etc. In the case of multiple data sources and multi-person collaboration, the construction of a genealogy knowledge graph involves the techniques of knowledge representation, knowledge acquisition, and knowledge fusion. In the knowledge fusion process, there are many situations such as the lack and chaos of a relationship, redundant entities, the isolation of some entities and knowledge fragments. How to effectively detect and process these problematic knowledge fragments is significant to the construction of a genealogy knowledge graph. In response to this problem, we propose a method for cleaning the problematic knowledge fragments in a genealogy knowledge graph. The method consists of three phases. In phase 1, we propose a method for detecting and analyzing the problematic knowledge fragments. In phase 2, we design a method for supplementing the entity-relationship of people for different error patterns and a method fusion method for the aligned entity. In phase 3, for the cleaning of isolated knowledge fragments, we propose an entity alignment method based on the father-son relationship and people's names and a connection method of isolated knowledge fragments. Finally, we conduct experiments on a family tree dataset of the Huapu System, and the experimental results indicate the effectiveness and practicality of the method.