Abstract: Intensive agricultural management is influential to soil microbiome and its functions. Based on a 36-year fertilization experiment at the Ministry of Agriculture Key Field Observation Station of Harbin Black Soil Ecological Environment, effects of four fertilization managements (CK: no fertilizer; NPK: mineral fertilizer; OM: organic fertilizer; MNPK: mineral NPK plus organic fertilizer) on soil fertility and microbial respiration were quantitively studied, and microbial community assembly mechanisms were analyzed using the high-throughput sequencing and community assembly models. Results show that long-term fertilization improved soil fertility, such as soil organic carbon, total nitrogen, available phosphorus and microbial activity. Soil microbial respiration was increased in the order of CK < NPK < OM < MNPK. Compared with CK (calculated in carbon, 186.9 μg·g^-1), soil microbial respiration in MNPK (calculated in carbon, 228.7 μg·g^-1) was increased by 22.4%. Linear discriminant analysis effect size (LEfSe) indicates that NPK and MNPK treatments had similar keystones including Dyella marensis, Bacillus megaterium and Herbaspirillum sp., while OM was predominated by Bacillus acidiceler and Bacillus megaterium. As compared with CK, long-term fertilization stimulated the growth of ammonia oxidizing bacteria (AOB) with the Nitrosospira-like AOB increased by 3.61 times in NPK treatment. The dominant phylotypes of ammonia oxidizing archaea (AOA) and nitrite oxidizing bacteria (NOB) were Nitrososphaera and Nitrospira, respectively. The co-occurrence network analysis revealed that soil microbial community in MNPK had the most closely links, with the proportion of positive links reached 99.6% versus 78.4% in NPK and 97.4% in OM. The analysis of β NTI indicates that long-term fertilization strengthened the deterministic processes of microbial community assembly, with the strongest determinism occurred in MNPK. Structural equation models (SEMs) further suggest strongly positive correlations between soil fertility improvement and microbial respiration (explaining > 90% of variation) among fertilization managements. This study demonstrates that long-term fertilization significantly stimulated the growth of functional microbiomes, altered community structure and improved soil fertility. Compared with NPK and OM, MNPK treatment was more efficient in enhancing soil fertility and stability of microbial community. As a whole, these results provide scientific basis for optimizing the efficient fertilization managements in black soils.