Lactic acid bacteria (LAB) inoculants are commonly used in silage production, yet their effects on silage containing antimicrobial components, such as those found in Leonurus japonicus, remain less explored. Herein, the harvested alfalfa were thoroughly mixed with dried Leonurus japonicus Houtt. (LJH) at a ratio of 9:1 on a fresh weight basis and treated without (CK) or with a lactic acid bacterial inoculant (L; Lentilactobacillus buchneri). The mixtures were stored under anaerobic conditions in vacuum-sealed polyethylene bags for 30 days at ambient temperature. The L-treated silage exhibited high levels of water-soluble carbohydrates (4.98% dry matter (DM)) and acid detergent fiber (27.88% DM). Compared to that of treatment CK, treatment with L increased the acetic acid content of the silage, as a result of increased (p < 0.05) bacterial dominance and decreased (p < 0.05) bacterial richness indices (e.g., Pielou’s E, Shannon, and Simpson) in the pre-storage period. However, these changes gradually reduced as the storage length increased. Treatment L reshaped the bacterial community structure of silage, by increasing the prevalence of Lactobacillus and reducing relative abundances of Enterococcus and Weissella. However, the principal coordinate and Bray–Curtis index analyses illustrated that samples from the L-treated silages exhibited similarities to the CK samples post-fermentation. Overall, the effect of LJH on LAB was only observed in the later stages of fermentation, which did not sufficiently change the silage quality. Hence, using LJH in silage is vital for clean livestock production without compromising the function of LAB when mixed with alfalfa silage.