Recent progress in sketch-based 3D shape retrieval creates a novel and user-friendly way to explore massive 3D shapes on the Internet. However, current methods on this topic rely on designing invariant features for both sketches and 3D shapes, or complex matching strategies. Therefore, they suffer from problems like arbitrary drawings and inconsistent viewpoints. To tackle this problem, we propose a probabilistic framework based on Multi-View Pairwise Relationship (MVPR) learning. Our framework includes multiple views of 3D shapes as the intermediate layer between sketches and 3D shapes, and transforms the original retrieval problem into the form of inferring pairwise relationship between sketches and views. We accomplish pairwise relationship inference by a novel MVPR net, which can automatically predict and merge the pairwise relationships between a sketch and multiple views, thus freeing us from exhaustively selecting the best view of 3D shapes. We also propose to learn robust features for sketches and views via fine-tuning pre-trained networks. Extensive experiments on a large dataset demonstrate that the proposed method can outperform state-of-the-art methods significantly.