Solid‐substrate electrospray ionization mass spectrometry is an important ambient ionization technology to simplify mass spectrometry analysis. Nowadays, its separation application has been reported increasingly, however, the detailed separation mechanism is still indistinct although the chromatographic effect was reported as a possible factor. In this study, substrate‐filled capillary electrospray ionization mass spectrometry was developed as an ideal model to investigate the separation mechanism using over thirty small molecules (neutral, basic, and weakly acidic) as model compounds with C18‐bonded silica gel and silica gel as the substrates. The chromatographic effect was validated by the negative t‐value of oil‐water distribution coefficient, and the electric field effect was verified by the paired t‐test (p < 0.01) between the retention times at 5.5 and 4.0 kV. A differential equation was proposed to quantify the compound retention under electric field. The quantitative method was validated to rapidly quantify proline (31.88 μg/mL) and hydroxyproline (20.71 μg/mL) in plasma with acceptable selectivity and accuracy. In conclusion, the separation mechanism of solid‐substrate electrospray ionization mass spectrometry was the combination of the chromatographic and electric field effects, which could provide theoretical guidance for the separation optimization, and also promote its applications in biological, pharmaceutical, forensic, food and environmental analyses, etc.