The pathological studies of cancer tissues and cell molecules could provide an early diagnosis for the treatment of cancer. In this work, we have designed a microfluidic surface extractor (MSE). The MSE has been coupled with electrospray mass spectrometry (extraction reagent, methanol; optimum flow rate, 0.5 mL/h) to analyze the phospholipid content of different tumor cells. Three types of cancer cell lines, including A549 cells, HepG2 cells, and U87 cells, were investigated, and the principle component analysis (PCA: linear discriminant analysis (LDA), PC1 97.2%; PC2, 2.8%) was carried out to analyze the difference in the lipid contents. The LDA revealed heterogeneity among the cancer cells. The designed MSE could have potential applications in the clinical analysis of cancer tissues.