Sketch-based image retrieval (SBIR) is a long-standing research topic in computer vision. Existing methods mainly focus on category-level or instance-level image retrieval. This paper investigates the fine-grained scene-level SBIR problem where a free-hand sketch depicting a scene is used to retrieve desired images. This problem is useful yet challenging mainly because of two entangled facts: 1) achieving an effective representation of the input query data and scene-level images is difficult as it requires to model the information across multiple modalities such as object layout, relative size and visual appearances, and 2) there is a great domain gap between the query sketch input and target images. We present SceneSketcher-v2, a Graph Convolutional Network (GCN) based architecture to address these challenges. SceneSketcher-v2 employs a carefully designed graph convolution network to fuse the multi-modality information in the query sketch and target images and uses a triplet training process and end-to-end training manner to alleviate the domain gap. Extensive experiments demonstrate SceneSketcher-v2 outperforms state-of-the-art scene-level SBIR models with a significant margin.