Diffusion of an analyte is one of the main determinants of reduced sensitivity in an electrospray ionization (ESI) source. In this work, the relative responses of compounds and their stable isotope-labeled (SIL) products in different injection modes were compared to investigate the diffusion behavior of analytes in ESI, without influence of other factors. Chloramphenicol (CAP) and D5 -CAP as well as melamine (Mel) and (13) C3 -Mel were used to illustrate the diffusion behavior in different operation modes and different ion sources, by comparing their relative responses in infusion mode and flow injection analysis (FIA) mode under variable temperature. In infusion mode, sample solution was introduced by syringe, and formed a stable and continuous signal. While in FIA mode, because of the huge difference in volume between the sample solution and the mobile phase, it is assumed that analyte ionizes and transmits in the gaseous phase created by the mobile phase. Analytes formed different concentration distributions in the two injection modes. The relative responses of CAP and D5 -CAP increased from 0.81 to 0.98 when the temperature was increased from 300°C to 650°C in infusion mode and decreased from 1.37 to 1.17 with increasing temperature in FIA mode. The opposite trends of the two injection modes were also obtained in positive operation modes and ion sources with different configuration. Opposite variation tendencies of relative responses of model samples and their stable isotope-labeled products with temperature were observed for infusion and FIA injection modes, indicating different diffusion behaviors in the two injection modes. These results provide a theoretical basis for ion source designing and better understanding of the ESI mechanism. Copyright © 2016 John Wiley & Sons, Ltd.