Small animal fluorescence imaging system is an important tool in life sciences and medicine research because of its in vivo and noninvasive imaging ability. But the relative low penetration depth of the visible light of existing small animal imaging systems, as well as the relative low signal-to-noise, prevents this technology from deep tissue imaging. Fluorescence single in the second near-infrared window (NIR II, 1000~1350 nm) could be utilized to improve the imaging depth due to the relative low tissue scattering. The presented work describes the design and performance evaluation of a near-infrared small animal fluorescence imaging system working in this particular spectrum window. Simulation experiments indicate that this imaging system achieves a relative high signal-to-noise ratio (57 dB) and large penetration depth (deeper than 10 mm). Vascular networks and organ of the mouse are clearly visualized using this imaging system by injection of Ag2S quantum dots (QD) emitting at 1200 nm.