In this study, a located fertilization experiment was conducted in a greenhouse for eight years, in which different treatments were set up as follows, no fertilization treatment (CK), four treatments of chemical fertilizer (N0PK, N1PK, N2PK, N3PK), manure treatment (M), and four treatments of chemical fertilizer combination with manure (MN0PK, MN1PK, MN2PK, MN3PK). The effects of long-term fertilization on soil total organic carbon (TOC), labile organic carbon (LOC) and its components (highly, moderately and lowly LOC) contents, and carbon pool management index (CPMI) and their profile distribution were studied. In the 0–50 cm layer, soil TOC and LOC contents of all fertilization measures showed a gradual decrease with the depth of soil layer. Compared with CK, the effects of application of chemical fertilizer (N0PK, N1PK, N2PK, N3PK) on soil TOC contents were not significant. The application of manure and the chemical fertilizer combination with manure (MN0PK, MN1PK, MN2PK, MN3PK) significantly increased soil TOC contents in the 0–20 cm layers (P<0.05), increased by 104.9%–135.3% and 97.6%–139.6%, respectively, and significantly increased the soil LOC contents in 0–50 cm soil layers (P<0.05), increased by 33.8%–235.5% and 33.8%–251.3%, respectively. In the 0–20 cm layer, the chemical fertilizer combination with manure significantly increased soil TOC contents compared with application of chemical fertilizer by 76.8%–174.7%, fixation ratios of organic carbon from manure under the medium application of chemical fertilizer combination with manure (MN2PK) treatment was the largest, with an average of 26.6%. In the 0–20 cm layer, the chemical fertilizer combination with manure significantly increased soil LOC and highly LOC contents compared with application of chemical fertilizer by 99.6%–259.4% and 122.2%–330.7%, respectively. The contents of soil LOC and its components were significantly linearly positively correlated with soil TOC content (P<0.05), the correlation coefficient between contents of highly LOC and TOC was the largest (r = 0.908). Compared with the application of the same chemical fertilizer, the chemical fertilizer combination with manure significantly increased CPMI of soil LOC and its highly and moderately components in the 0–20 cm layer (P<0.05), CPMI of LOC, highly and moderately LOC increased with the increase of nitrogen application rate. In summary, under the condition of greenhouse tomato cultivation for eight years, the chemical fertilizer combination with manure significantly increased the contents of soil TOC, LOC and its highly components in the 0–20 cm layer, and CPMI of soil LOC and its highly components were significantly improved. The chemical fertilizer combination with manure increased soil fertility and improved soil quality. Medium-weight treatments of chemical fertilizer combination with manure treatments (MN2PK) is a reasonable management practice for sustainable production of tomatoes in greenhouse.