To clarify the contribution of the bridging effect from three metal cations (Ksup.+, Mnsup.2+, and Fesup.3+) on the humification of lignin-rich Tilia wood shavings and further enrich the theory of lignin humification, an indoor incubation method with constant temperature and humidity was adopted. Ksup.+, Mnsup.2+, and Fesup.3+ served as additives, with CK as the control for studying the differential influence of metal cations with different valences on the humus composition of dark-brown soil mixed with Tilia wood shavings. The change in the C contents of water-soluble substance (Csub.WSS), humic-extracted acid (Csub.HE) and humin (Csub.Hu), ∆logK value of HE, atomic ratio and FTIR spectra of humic acid (HA), and the ratio of C content of humic acid to fulvic acid (Csub.HA/Csub.FA) of dark-brown soil mixed with Tilia wood shavings were analyzed after 0, 30, 80, and 150 days of incubation, and the following conclusions were reached: (1) The addition of metal cations, regardless of their valence, could effectively improve the microbial utilization and consumption of WSS, and the effect was as follows: Fesup.3+ > Mnsup.2+ > Ksup.+. The addition of three metal cations could effectively inhibit mineralization and reduce the loss of TOC, and the effect could be seen as follows: Fesup.3+ > Mnsup.2+ > Ksup.+. (2) Although the Csub.HE content first decreased and then increased with incubation, the addition of Fesup.3+ and Mnsup.2+ ions increased the Csub.HE content, showing that Fesup.3+ > Mnsup.2+, and Ksup.+ ions had no significant effect. Throughout the incubation, the structure of HE molecules changed first via a complex process and then through a simple process. Comparing the change before and after the incubation, the overall structure of HE molecules tended to be simpler with the CK control, and HE became more complicated with the addition of Fesup.3+ and Mnsup.2+; however, the addition of Ksup.+ had little effect on the structure of HE molecules. (3) At the end of the incubation, the addition of Fesup.3+, Mnsup.2+, and Ksup.+ ions strengthened the molecular condensation of HA and its aromatization degree, while the CK control without any added metal cations caused HA molecules to decompose and obtain a greater aliphatic degree. In addition, the number of O-containing functional groups and N-containing compounds in HA molecules increased to varying degrees regardless of which metal cation was added. The decomposition of Tilia wood chips led to a partial entry of the decomposition products into the HA component, which was then reconsumed by continuous mineralization. After incubation, the polysaccharides in HA molecules were consumed only with the addition of Mnsup.2+ ions. Fesup.3+ and Mnsup.2+ ions had greater advantages in increasing the Csub.HA/Csub.FA ratio and improving the humus quality than Ksup.+ ions. (4) The addition of metal cations could effectively inhibit the mineralization and decomposition of the Hu component, among which Fesup.3+ ions had the most significant effect, followed by Mnsup.2+ ions. Compared to monovalent cations (Ksup.+), polyvalent cations (Fesup.3+ and Mnsup.2+) had the advantage of a bridging effect, and their addition promoted the microbial utilization of WSS, effectively reduced the loss of TOC, increased the Csub.HE content, complicated its molecular structure, improved the humus quality, and inhibited the decomposition of Hu. Regardless of which metal cation was added, the degree of molecular polycondensation and aromatization of HA was enhanced, and the number of O-functional groups and N-containing compounds in HA molecules increased.