As a rate-limiting enzyme in the major pathway of l-tryptophan catabolism, indoleamine 2, 3-dioxygenase 1 (IDO1) has been regarded as a potential target for the treatment of a variety of diseases. To identify the key molecular features and extend the structural variety of IDO1 inhibitors, a ferrous binding group (FBG)-based 3D-QSAR pharmacophore model was constructed, validated and used for virtual screening herein. The Specs database was initially filtered based on drug-like rules, and was subsequently screened by the pharmacophore model. Molecular docking simulations and similarity analysis were then followed to prioritize twenty compounds for biological tests. Among them, compound VS-13 exhibited moderate inhibitory activity against IDO1, and could be subjected to further structure-activity relationship studies and structural optimization.