Oxylipins are diverse bioactive signaling molecules, which occur in very low concentrations in complex matrices, posing challenges in achieving consistent and sensitive analysis. UHPLC-MS/MS is the preferred technique to separate and quantify these molecules, often optimized using a time-consuming trial-and-error approach. In this study, we applied the design of experiments (DoE) approach to systematically investigate the ionization properties of multiple oxylipin species. Fractional factorial and central composite designs were employed to detect relevant instrument parameters and optimize signal intensity in ESI-MS/MS analysis. Response surface modeling revealed distinct ionization and fragmentation behaviors between polar and apolar oxylipins, driven by their responses to interface temperature and collision-induced dissociation (CID) gas pressure. Particularly, prostaglandins and lipoxins benefit from higher CID gas pressure and lower temperatures compared to the lipophilic HODEs and HETEs to achieve optimal intensity in multiple reaction monitoring analysis. While global source parameters were optimized, analyte-specific entrance/exit potentials and collision energies required individual adjustments. The final method was applied to analyze seven oxylipin classes including leukotrienes, prostaglandins, lipoxins, resolvins, HETEs, HODE