Abstract The effect of ambient air as an unavoidable problem for atmospheric pressure plasma jet (APPJ) applications has attracted a lot of interest, especially when the specific scenarios are highly sensitive to ambient species such as the biomedical process. The coaxial double-tube device is a promising method for controlling the ambient species into the jet effluent and thus the chemical properties of the jet effluent. In this work, the discharge characteristics and plasma chemistry of the coaxial double-tube helium APPJ at different shielding gas (SG) flow rates are studied numerically. An experiment on optical images of the discharge is conducted to illustratively validate the variation of the (main) discharge channel widths in the model as the SG flow rate varies. The results illustrate that the discharge is enhanced at the high flow rate, while it shows the weaker discharge behavior at the low flow rate as well as that without SG. The analysis of the dielectric plate surface indicates that the species fluxes to the dielectric plate significantly increase with the increases in the flow rate, which can be attributed to the wider (main) discharge channel. Moreover, to further explore the impact of the SG on the effluent chemistry, the ions fluxes on the surfaces of the main discharge channel and the discharge channel are distinguished and discussed. The analysis shows the great difference in the ions fluxes affected by the flow rate between the two discharge channels. In summary, advancing the knowledge that the flow rate of the SG has an impact on the discharge behavior, this study further reveals that different discharge positions greatly influence the production of nitrogen/oxygen species. This work enables the previously elusive account of the effect of SG and may open new opportunities for the further application of coaxial double-tube APPJ.