Elucidating the spatial-biochemical organization of the brain across different scales produces invaluable insight into the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive chemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping via MEISTER, an integrative experimental and computational mass spectrometry framework. MEISTER integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating 3D molecular distributions, and a data integration method fitting cell-specific mass spectra to 3D data sets. We imaged detailed lipid profiles in tissues with data sets containing millions of pixels, and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents, and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future developments of multiscale technologies for biochemical characterization of the brain.