This paper describes graph-based Wave Function Collapse algorithm for procedural content generation. The goal of this system is to enable a game designer to procedurally create key content elements in the game level through simple association rule input. To do this, we propose a graph-based data structure that can be easily integrated with a navigation mesh data structure in a three-dimensional world. With our system, if the user inputs the minimum association rule, it is possible to effectively perform procedural content generation in the three-dimensional world. The experimental results show that the Wave Function Collapse algorithm, which is a texture synthesis algorithm, can be extended to non-grid shape content with high controllability and scalability.