Precise medicine recommendations provide more effective treatments and cause fewer drug side effects. A key step is to understand the mechanistic relationships among drugs, targets, and diseases. Tensor-based models have the ability to explore relationships of drug-target-disease based on large amount of labeled data. However, existing tensor models fail to capture complex nonlinear dependencies among tensor data. In addition, rich medical knowledge are far less studied, which may lead to unsatisfied results. Here we propose a Neural Tensor Network (NeurTN) to assist personalized medicine treatments. NeurTN seamlessly combines tensor algebra and deep neural networks, which offers a more powerful way to capture the nonlinear relationships among drugs, targets, and diseases. To leverage medical knowledge, we augment NeurTN with geometric neural networks to capture the structural information of both drugs’ chemical structures and targets’ sequences. Extensive experiments on real-world datasets demonstrate the effectiveness of the NeurTN model.