Abstract: The study aimed to determine the optimal ratio of biogas slurry to chemical fertilizer and the effects of biogas slurry combined with chemical fertilizer on Allium fistulosum yields, soil nutrients levels, microorganism contents, and enzyme activities. The field experiment comprised six treatments: no fertilization (CK), chemical fertilizer (CF), 25% substitution inorganic N by biogas slurry N (25BS), 50% substitution inorganic N by biogas slurry N (50BS), 75% substitution inorganic N by biogas slurry N (75BS), and 100% substitution inorganic N by biogas slurry N (100BS). A. fistulosum yields, soil nutrients contents, phospholipid fatty acids (PLFA) contents, and activities of enzymes involved in C, N, and P cycling were investigated. Using the partial least squares path model (PLS-PM), the variations in these parameters to elucidate their internal correlations were explored. The results indicated that CF and biogas slurry (25BS, 50BS, 75BS, and 100BS) treatments significantly increased A. fistulosum yield compared to CK (P<0.05), with increases of 37.2%, 75.9%, 118.9%, 99.8%, and 59.3%, respectively. Furthermore, as the substitution percentage of inorganic N by biogas slurry N increased, the yields showed a tendency of increasing initially and then decreasing, with the highest yield of 59.9 t·hm⁻² observed for the 50BS treatment. The application of biogas slurry was effective in improving soil nutrients contents. Compared to CK, the biogas slurry significantly increased the contents of soil organic carbon (SOC), total nitrogen (TN), ammoniacal nitrogen (NH₄⁺), nitrate nitrogen (NO₃⁻), available phosphorus (AP), and available potassium by 19.5%–65.8%, 40.5%–69.6%, 26.8%–77.4%, 30.1%–41.9%, 10.5%–40.6%, and 5.4%–8.5%, respectively. The application of biogas slurry resulted in a notable enhancement in soil microbial contents and enzymes activities. Compared to CK, the biogas slurry significantly increased the PLFA contents of bacteria, fungi, and actinomycetes (P<0.05), while concurrently reducing the ratio of gram-positive to gram-negative bacteria. This shift is advantageous for improving the activities of enzymes involved in C, N, and P cycling. However, with an increasing ratio of inorganic N substitution by biogas slurry, the number of bacteria, gram-positive bacteria, fungi, total PLFA content, and enzymes activities involved in C, N, and P cycling exhibited an initial increase followed by a subsequent decrease. The results of PLS-PM indicated that the observed increase in A. fistulosum yields after biogas slurry application could be attributed to the improvements in SOC, TN, NH₄⁺, NO₃^– and AP contents, microbial contents, and the enhanced activities of enzymes involved in N cycling. Nevertheless, the excessive application of biogas slurry led to elevated soil electrical conductivity (EC), which inhibited microbial activities and ultimately reduced A. fistulosum yields. In conclusion, this study illustrated that the temporary utilization of biogas slurry contributed to the enhancement of A. fistulosum yields, effective improvement of soil nutrient levels, and promotion of soil microbial contents and enzymes activities. Notably, the optimal substitution percentage of inorganic N by biogas slurry was 50% to achieve the highest improvement. However, biogas slurry cannot completely substitute chemical fertilizers because its excessive use may lead to an increase in soil salinity, adversely affecting the growth of A. fistulosum and microorganisms.