Molecular imaging has become a research focus in recent years, which provides an effective information acquisition, analysis and processing methodology at cellular and molecular levels for biomedical study. As an important molecular imaging technique, optical molecular imaging, especially fluorescence and bioluminescence imaging, has attracted remarkable attention in tumor study and drug development for its excellent performance, non-radiativity and high cost-effectiveness in comparison with conventional imaging modalities. Generally speaking, optical molecular imaging is regarded as the combination of traditional medical imaging technology and modern molecular biology, in which the advanced optics, biology, information, medicine, and other techniques are being married to non-invasively obtain in vivo physiological and pathological information sensitively, quantitatively, and specifically. Further, with the research of imaging theories, algorithms and molecular probes, optical imaging systems have been rapidly developed for biomedical study in molecular imaging discipline, including planar imaging systems, tomographic imaging systems, and multimodality fusion systems, and so on. This review focuses on some typical optical molecular imaging systems, especially for in vivo small animal use. It also provides a brief discussion on the future development and application of the optical molecular imaging systems.