Partial substitution of inorganic fertilizers with organic amendments is an important agricultural management practice.  An 11-year field experiment (22 cropping periods) was carried out to analyze the impacts of different partial substitution treatments on crop yields and the transformation of nitrogen fractions in greenhouse vegetable soil.  Four treatments with equal N, P₂O₅, and K₂O inputs were selected, including complete inorganic fertilizer N (CN), 50% inorganic fertilizer N plus 50% pig manure N (CPN), 50% inorganic fertilizer N plus 25% pig manure N and 25% corn straw N (CPSN), and 50% inorganic fertilizer N plus 50% corn straw N (CSN).  Organic substitution treatments tended to increase crop yields since the 6th cropping period compared to the CN treatment.  From the 8th to the 22nd cropping periods, the highest yields were observed in the CPSN treatment where yields were 7.5–11.1% greater than in CN treatment.  After 11-year fertilization, compared to CN, organic substitution treatments significantly increased the concentrations of NO₃^–-N, NH₄⁺-N, acid hydrolysis ammonium-N (AHAN), amino acid-N (AAN), amino sugar-N (ASN), and acid hydrolysis unknown-N (AHUN) in soil by 45.0–69.4, 32.8–58.1, 49.3–66.6, 62.0–69.5, 34.5–100.3, and 109.2–172.9%, respectively.  Redundancy analysis indicated that soil C/N and OC concentration significantly affected the distribution of N fractions.  The highest concentrations of NO₃^–-N, AHAN, AAN, AHUN were found in the CPSN treatment.  Organic substitution treatments increased the activities of β-glucosidase, β-cellobiosidase, N-acetyl-glucosamidase, L-aminopeptidase, and phosphatase in the soil.  Organic substitution treatments reduced vector length and increased vector angle, indicating alleviation of constraints of C and N on soil microorganisms.  Organic substitution treatments increased the total concentrations of phospholipid fatty acids (PLFAs) in the soil by 109.9–205.3%, and increased the relative abundance of G⁺ bacteria and fungi taxa, but decreased the relative abundance of G^– bacteria, total bacteria, and actinomycetes.  Overall, long-term organic substitution management increased soil OC concentration, C/N, and the microbial population, the latter in turn positively influenced soil enzyme activity.  Enhanced microorganism numbers and enzyme activity enhanced soil N sequestration by transforming inorganic N to acid hydrolysis-N (AHN), and enhanced soil N supply capacity by activating non-acid hydrolysis-N (NAHN) to AHN, thus improving vegetable yield.  Application of inorganic fertilizer, manure, and straw was a more effective fertilization model for achieving sustainable greenhouse vegetable production than application of inorganic fertilizer alone.