Solid-state anaerobic digestion is easily inhibited by high volatile fatty acid induced by high total solids, although it is a promising technology. Previous studies on volatile fatty acid inhibition mainly focused on total solid content, co-digestion substrates, and external additives. The present study proposed a new inoculation method named layer inoculation and compared it to premixing inoculation in the solid-state anaerobic digestion of pig manure and maize straw. The results showed that the cumulative CH₄ yields from layer inoculation (211.5 mL/g-VS) were 5.64 times more than premixing inoculation (37.5 mL/g-VS) under a low inoculation ratio (25%), with the values of total volatile fatty acid being greater than 30.0 mg/g. The concentrations of total VFAs and acetic acid from layer inoculation decreased dramatically during days 18–43. Layer inoculation also showed wider specific methane yield peaks and shorter startup times than premixing inoculation. Methanosphaerula and Methanothrix were the most dominant genera, while the genus Methanosphaerula did not correlate with volatile fatty acids, pH, or total ammonia nitrogen. The hydrogenotrophic methanogen pathway was predominant during solid-state anaerobic digestion; the shift from hydrogenotrophic to acetoclastic occurred in premixing inoculation, and it was stable in layer inoculation (61.20–68.88%). Overall, layer inoculation can effectively enhance methane production under high volatile fatty acid concentrations compared with premixing inoculation.