Optical microscopy has been widely used as a versatile tool in biological research. However, its penetration depth and spatial resolution are desperately limited by light scattering during deep propagation in turbid medium. Here, we implement near-infrared second window (1000-1700 nm) multifocal structured illumination microscopy (NIR-II MSIM) capable of deep penetration, high contrast, and enhanced spatial resolution. Raster-scanning multifocal illumination patterns ensure homogeneous illumination of the sample. By integrating NIR-II photoemission into multifocal photoexcitation, NIR-II MSIM affords deep imaging with improved lateral resolution (∼1.49 µm) at a depth of 2.5 mm in an Intralipid/agar phantom and outstanding contrast. Additionally, imaging at longer wavelength in the NIR-II region shows superior performance. This NIR-II MSIM system will afford a promising platform for studying physiological phenomena in turbid specimens in the future.