With the gradual development of the network, RDF graphs have become more and more complex as the scale of data increases; how to perform more effective query for massive RDF graphs is a hot topic of continuous research. The traditional methods of graph query and graph traversal produce great redundancy of intermediate results, and processing subgraph collection queries in stand-alone mode cannot perform efficient matching when the amount of data is extremely large. Moreover, when processing subgraph collection queries, it is necessary to iterate the query graph multiple times in the query of the common subgraph, and the execution efficiency is not high. In response to the above problems, a distributed query strategy of RDF subgraph set based on composite relation tree is proposed. Firstly, a corresponding composite relationship is established for RDF subgraph set, then the composite relation graph is clipped, and the redundant nodes and edges of the composite relation graph are deleted to obtain the composite relation tree. Finally, using the composite relation tree, a MapReduce-based RDF subgraph set query method is proposed, which can use parallel in the computing environment, the distributed query batch processing is performed on the RDF subgraph set, and the query result of the RDF subgraph set is obtained by traversing the composite relation tree. The experimental results show that the algorithm proposed in this paper can improve the query efficiency of RDF subgraph set.