Organic manure is one of the most important factors to maintain soil fertility and achieve high yield in greenhouse vegetable production. Effects of organic manure, mineral nitrogen application and wheat straw incorporation on C cycling was investigated based on a six-year greenhouse tomato experiment in Shandong Province, northern China. In contrast to the amount of 0.14 t C ha -1 a-1 contributed by root residue, chicken manure, with 3.80 t C ha-1 a-1, was the dominant C supplement. Without any manure application, soil organic carbon and soil non-labile carbon fraction significantly decreased after 6 years of intensive tomato production. High chicken manure applied rates ranging from 13 to 20 t ha-1 a -1 only could maintain SOC content at their initial levels in the greenhouse. Based on the organic manure application, little effect of different mineral N application rate on SOC content was observed. Manure and straw incorporation significantly enhanced soil respiration rate, especially for straw incorporation, which led to higher negative net ecosystem productivity. Meanwhile no significant increase of SOC content was observed with manure and straw incorporation. High organic carbon decomposition rate due to year-round high temperature and moisture and excessive manure with low C/N ratio might be the dominant reason for the low accumulated rate of soil organic matter in this greenhouse tomato planting system. How to improve the soil organic matter further will be a great challenge in greenhouse vegetable production.