In this study, an open-tubular capillary electrochromatography (OT-CEC) column with a monolithic layer of molecularly imprinted polymer (MIP) based on methacrylic acid, ethylene glycol dimethacrylate, and 4-styrenesulfonic acid was utilized for the simultaneous separation and characterization of phospholipid (PL) molecular structures by interfacing with electrospray ionization-tandem mass spectrometry (ESI-MS-MS). Introducing an MIP-based monolith along with charged species at the OT column made it possible to separate PL molecules based on differences in head groups and acyl chain lengths in CEC. For the interface of OT-CEC with ESI-MS-MS, a simple nanospray interface utilizing a sheath flow was developed and the resulting OT-CEC-ESI-MS-MS was able to separate PL standards (phosphatidylserines, phosphatidylethanolamines, phosphatidylglycerols, phosphatidic acid, and lysophosphatidylglycerols). The developed method was applied to human urinary lipid extracts, and resulted in the separation and structural identification of 18 molecules by data-dependent collision-induced dissociation.