Recently, real-world recommendation systems need to deal with millions of candidates. It is extremely challenging to conduct sophisticated end-to-end algorithms on the entire corpus due to the tremendous computation costs. Therefore, conventional recommendation systems usually contain two modules. The matching module focuses on the coverage, which aims to efficiently retrieve hundreds of items from large corpora, while the ranking module generates specific ranks for these items. Recommendation diversity is an essential factor that impacts user experience. Most efforts have explored recommendation diversity in ranking, while the matching module should take more responsibility for diversity. In this paper, we propose a novel Heterogeneous graph neural network framework for diversified recommendation (GraphDR) in matching to improve both recommendation accuracy and diversity. Specifically, GraphDR builds a huge heterogeneous preference network to record different types of user preferences, and conduct a field-level heterogeneous graph attention network for node aggregation. We also innovatively conduct a neighbor-similarity based loss to balance both recommendation accuracy and diversity for the diversified matching task. In experiments, we conduct extensive online and offline evaluations on a real-world recommendation system with various accuracy and diversity metrics and achieve significant improvements. We also conduct model analyses and case study for a better understanding of our model. Moreover, GraphDR has been deployed on a well-known recommendation system, which affects millions of users. The source code will be released.