We present a laser scanning reflection-matrix microscopy combining the scanning of laser focus and the wide-field mapping of the electric field of the backscattered waves for eliminating higher-order aberrations even in the presence of strong multiple light scattering noise. Unlike conventional confocal laser scanning microscopy, we record the amplitude and phase maps of reflected waves from the sample not only at the confocal pinhole, but also at other non-confocal points. These additional measurements lead us to constructing a time-resolved reflection matrix, with which the sample-induced aberrations for the illumination and detection pathways are separately identified and corrected. We realized in vivo reflectance imaging of myelinated axons through an intact skull of a living mouse with the spatial resolution close to the ideal diffraction limit. Furthermore, we demonstrated near-diffraction-limited multiphoton imaging through an intact skull by physically correcting the aberrations identified from the reflection matrix. The proposed method is expected to extend the range of applications, where the knowledge of the detailed microscopic information deep within biological tissues is critical.