Very recently, experimental evidence showed that the hydrogen is retained in dithiol-terminated single-molecule junction under the widely adopted preparation conditions, which is in contrast to the accepted view [Nat. Chem.11 351 (2019)]. However, the hydrogen is generally assumed to be lost in the previous physical models of single-molecule junctions. Whether the retention of the hydrogen at the gold—sulfur interface exerts a significant effect on the theoretical prediction of spin transport properties is an open question. Therefore, here in this paper we carry out a comparative study of spin transport in M-tetraphenylporphyrin-based (M = V, Cr, Mn, Fe, and Co; M-TPP) single-molecule junction through Au–SR and Au–S(H)R bondings. The results show that the hydrogen at the gold–sulfur interface may dramatically affect the spin-filtering efficiency of M-TPP-based single-molecule junction, depending on the type of transition metal ions embedded into porphyrin ring. Moreover, we find that for the Co-TPP-based molecular junction, the hydrogen at the gold–sulfur interface has no obvious effect on transmission at the Fermi level, but it has a significant effect on the spin-dependent transmission dip induced by the quantum interference on the occupied side. Thus the fate of hydrogen should be concerned in the physical model according to the actual preparation condition, which is important for our fundamental understanding of spin transport in the single-molecule junctions. Our work also provides guidance in how to experimentally identify the nature of gold–sulfur interface in the single-molecule junction with spin-polarized transport.