16MnR and SPV50Q low-alloyed steels, which have ferrite-pearlite and tempered martensite microstructures, respectively, are widely used to fabricate storage tanks for liquefied petroleum gas. However, during the process of operation, some cracks often occur on tanks made by these steels due to the presence of hydrogen, especially on weldments. The occurrence of this cracking is closely related to the diffusion and permeation of hydrogen in the steels. In order to explore the effect of different microstructures on hydrogen permeation and compare the hydrogen permeability of these two weldments, measurements were conducted on various metals (base metal-BM, heat-affected zone-HAZ, and welded metal-WM) cut from 16MnR and SPV50Q weldments by using electrochemical permeation tests. The results show that the microstructure has an important effect on hydrogen permeability. For 16MnR steel weldment, the diffusion coefficient of BM is the minimum due to the presence of the strong hydrogen traps in the interface between banded pearlite and matrix as well as the interface between inclusion and matrix. The microstructure of WM provides great grain boundary area as a hydrogen diffusion path and makes hydrogen easily diffuse, which results in the maximum permeation rate and diffusion coefficient. The fine-grained microstructure of normalized zone in HAZ acts as barriers for the hydrogen diffusion, which makes the permeation rate and diffusion coefficient of HAZ located between those of BM and WM. Similarly, for SPV50Q weldment, the permeation rate and diffusion coefficient increase in the order of BM, HAZ and WM. Those of BM are the minimum, which is correlated with the strong hydrogen trap due to the large quantities of dislocation within the lath martensite. Those of WM are the maximum for its strongly hydrogen diffusion path like WM of 16MnR weldment. As comparing the hydrogen permeability of 16MnR and SPV50Q weldment, the corresponding metals of the former always have greater permeation rate and diffusion coefficient than those of the latter, which is also due to its intrinsic microstructures.