Large-scale microscopy approaches are transforming brain imaging, but currently lack efficient multicolor contrast modalities. We address this issue by introducing chromatic multiphoton serial (ChroMS) microscopy, a method combining multicolor multiphoton excitation through wavelength mixing and microtome-assisted serial block-face image acquisition. This approach delivers large-scale micrometric imaging of spectrally distinct fluorescent proteins with constant micrometer-scale resolution and sub-micron channel registration over the entire imaged volume. We achieve multicolor 3D imaging over several cubic millimeters and brain-wide serial 2D multicolor imaging. We illustrate the potential of this method for several novel types of measurements interesting for region-scale or whole brain studies: (i) color-based analysis of astrocyte morphology and spatial interactions in the mouse cerebral cortex, (ii) tracing of densely labeled neurons, and (iii) brain-wide mapping of axonal projections labeled with distinct tracers.