Recently, high quality MgB2 single junctions and junction arrays fabricated by Focused Helium Ion Beam irradiation (He-FIB) have been reported. However, the effects of irradiation doses and substrates on junction properties have not been analysed systematically. In this work, 30 nm MgB2 thin films were deposited on SiC (0001) and MgO (111) substrates using Hybrid Physical–Chemical Vapour Deposition (HPCVD) technique and then etched into 2–4 μm wide microbridges. 2000–6000 ions/nm doses of He-FIB were irradiated across these microbridges, creating narrow junction barriers. R–T curves exhibit a clear foot-like structure that enlarges as irradiation dose increases. Temperature dependence of junction properties (critical current Ic, junction normal state resistance Rn, characteristic voltage Vc) shows that all junctions in our experiment exhibit superconductor–normal–superconductor (SNS) like behaviour and higher irradiation doses create thicker junction barriers. Furthermore, we analyse junction properties dependence on irradiation doses which yields an exponential change law. Finally, Fraunhofer diffraction-like patterns and Shapiro steps of junctions are also measured. Our results show MgB2 Josephson Junctions with adjustable properties can be fabricated by He-FIB on SiC and MgO substrates, which provides a solid foundation for future application devices research.