In order to know the ecological characteristics of soil nematodes in organic agriculture, soil nematode abundance and diversity were compared in 9 organic cultivation and conventional cultivation soils from East, Central and West China during the period of 2013—2014. The results showed that 27 families and 57 genera of nematodes were identified. The total number of nematodes was about 1 037 individuals per 100 g dry soil with organic management, remarkably different from that with conventional management, so was the bacterivores. The bacterivorous nematodes (Cephalobus & Eucephalobus) and the phytophagous nematodes (Aphelenchoides & Filenchus) existed in all the organic sampling sites. From the aspect of nematode ecological indices, overall, Wasilewska index (WI) and Nematode Channel Ratio (NCR) of the organic farming system indicated that soil conditions were relatively healthy with bacteria dominant in the decomposition of the soil debritus food web. While no significant difference was found between the organic and conventional managements in other ecological indices. Significant correlations were observed between oil physicochemical characteristics and the nematode numbers, WI, MI, PPI.