Soil samples within 0 – 20 cm and 20 – 40 cm were collected from different irrigation modes (furrow irrigation (FI), drip irrigation (DI) and subsurface irrigation (SI)) in the same protected field where the irrigation experiment was continued for 13 years to research the effects of different irrigation modes on black carbon (BC) and the relationship between black carbon and other organic carbon fractions in greenhouse. The results suggested that the contents of TOC, BC and SHC all showed the biggest amount in 0 – 20 cm and there were significant differences within different layers for irrigation modes. The contents of TOC and BC within 0 – 20 cm and 20 – 40 cm generally presented the trend DI > SI > FI, while that of SHC was FI>DI>SI. The content ranges of TOC, BC and SHC were 21.15 – 25.53, 5.30 – 7.59 and 3.64 – 5.75 g/kg in 0 – 20 cm and were 11.62 – 17.55, 3.39 – 5.40 and 3.54 – 3.83 g/kg in 20 – 40 cm, respectively. The contents of BC and SHC accounted for 22.81% – 30.85% and 16.60% – 33.03% of TOC respectively within 0 – 40 cm soil layer. There were significant positive correlation between soil BC and TOC, but not between BC and SHC.