In this work, an on-line preconcentration capillary electrochromatographic (CEC) separation coupled with atmospheric pressure chemical ionization-mass spectrometry (APCI-MS) was used for 16 PAHs analyses, in which poly(stearyl methacrylate-divinylbenzene) (poly(SMA-DVB)) monolith was used as the separation column. With variations in the effective length of poly(SMA-DVB) monolith as well as the volume fraction of acetonitrile (ACN) in the mobile phase, both separation and resolution were improved. A poly(SMA-DVB) monolith of 50-cm effective length (i.e. 50-cm column length filled with polymer) and a two-step step-gradient elution (by changing the ACN levels of the mobile phase starting with an initial of 70% up to 80% with 30-min time interval), which provided baseline separation for PAHs solutes (except for chrysene and benzo[a]anthracene) within 50min, were employed as the optimal chromatographic conditions. In contrast to the other mass spectrometer parameters (nebulizer gas pressure, vaporizer temperature, corona current) as well as on-line preconcentration parameter (the ACN level in the sample matrix), the sheath liquid composition (methanol/water in the ratio of 3:1) and the sample injection time (40min) were found as the predominant factors that control the sensitivity of PAHs determination. Finally, this on-line preconcentration CEC–APCI-MS method determined PAH residues in seafood samples successfully with as low as 10ng/g level.