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Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a powerful tool for the characterization and localization of analytes without the need for extraction, purification, separation or labeling of samples. However, in tissue sections the most abundant lipids, phosphatidylcholines (PCs), could suppress the signals of other classes of coexisting lipids. In this work, polydopamine (PDA)-capped AgNPs (AgNPs@PDA) were synthesized as a matrix of MALDI MSI to analyze lipids in both positive and negative ion modes. By adjusting the thickness of the PDA layer, the signal of silver cluster ions of AgNPs@PDA was effectively controlled, and the ability of AgNPs@PDA serving as a matrix was optimized. More interestingly, using AgNPs@PDA as a matrix, the sensitivity of PCs was dramatically decreased, and the PC signals were greatly suppressed, while for other lipids (including PE, HexCer, PS, PI, PIP, and ST), they were just the opposite. The reason, we believe, is related to the positively charged surface of AgNPs@PDA, and the polyhydroxy and amino groups of PDA. Benefitting from the suppression of the signals of PCs and the improvement of detection sensitivity of other lipids, 58 glycerophospholipids and 25 sphingolipids in brain tissue sections could be imaged in one run with AgNPs@PDA as a matrix by MALDI MSI, much better than when using traditional organic matrices 2,5-dihydroxybenzoic acid and 9-aminoacridine.