Fact-based Visual Question Answering (FVQA) requires external knowledge beyond the visible content to answer questions about an image. This ability is challenging but indispensable to achieve general VQA. One limitation of existing FVQA solutions is that they jointly embed all kinds of information without fine-grained selection, which introduces unexpected noises for reasoning the final answer. How to capture the question-oriented and information-complementary evidence remains a key challenge to solve the problem. In this paper, we depict an image by a multi-modal heterogeneous graph, which contains multiple layers of information corresponding to the visual, semantic and factual features. On top of the multi-layer graph representations, we propose a modality-aware heterogeneous graph convolutional network to capture evidence from different layers that is most relevant to the given question. Specifically, the intra-modal graph convolution selects evidence from each modality and cross-modal graph convolution aggregates relevant information across different graph layers. By stacking this process multiple times, our model performs iterative reasoning across three modalities and predicts the optimal answer by analyzing all question-oriented evidence. We achieve a new state-of-the-art performance on the FVQA task and demonstrate the effectiveness and interpretability of our model with extensive experiments.