Phospholipids are the major components of cellular membranes and possess important biological roles. Despite their significance in diagnosis and therapeutic application in various diseases, systematic profiling of phospholipids remains challenging due to time-consuming sample preparation and their inherent structure complexity. Taking advantages of complementary, simple, and fast structural analysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Fourier transform infrared spectroscopy (FTIR), we reported a nanoprobe-based dual detection strategy for large-scale phospholipid profiling. Based on electrostatic interaction between nitrilotriacetic acid (NTA) chelated iron ion and phosphate head on phospholipids, we developed an NTA-decorated magnetic nanoparticle (MNP)-based strategy for enrichment of phospholipids from lung cancer cell lines. Compared to the conventional liquid–liquid extraction, NTA@MNP nanoprobe enrichment demonstrated 2.6-fold more identified phospholipids. By direct on-particle analysis, FTIR confirmed the P-O-C and phosphate stretching characteristic of the phospholipid head group, and MALDI-TOF MS identified a total of 59 phospholipids from PC9 and A549 lung cancer cells. Comparing the variation of phospholipids between two cell lines, we identified significantly more phospholipids in the PC9 cells (49) compared to 35 phospholipids in the A549 cells. The comparison also revealed 24 and 10 cell line-specific phospholipids in the PC9 and A549 cells, respectively. Given the demonstrated rapid enrichment and unambiguous identification of phospholipids at cellular levels, the developed approach can provide systematic profiling to study the under-explored phospholipid species.