Confocal laser scanning microscopy (CLSM) is expected to exhibit a better imaging performance in the second near-infrared (NIR-II) windows with weak tissue scattering and autofluorescence. However, the indium gallium arsenide (InGaAs) detectors currently used for imaging in the NIR-II region are prohibitively expensive, hampering its extensive biomedical applications. In this study, a novel NIR-II CLSM system is developed by using the inexpensive silicon photomultiplier (SiPM) that can perform the multicolor biological imaging in vivo. Using IR-780 iodide as the contrast agent, the NIR-II imaging capability of constructed CLSM is inspected, demonstrating a spatial resolution of 1.68 µm (close to the diffraction limit) and a fluorophore detection sensitivity as low as 100 nm. In particular, it is discovered that the multicolor imaging performance in both NIR-I and NIR-II windows is comparable to those from multialkali and InGaAs photomultiplier tubes. In addition, 3D NIR-II CLSM is also conducted for in vivo imaging of the vascular structure in mouse ear and subcutaneous tumors. To the best of authors’ knowledge, this is the first time that a low-cost detector based on a SiPM has been used for microscopic imaging of trailing fluorescence signals in the NIR-II region of an NIR fluorescent probe.