Soil fumigation with methyl bromide (MB) has been effectively used for decades to control soil borne pathogens. However, because of ozone-depleting and negative effects on soil beneficial organism, its use has been limited. Recently, several researches have been reported on the use of alternative technologies to replace MB. In this sense, we have studied the impact of MB on functional groups and the community structure in the soil food web with objective to provide the theory support for the selection of MB alternative technologies. The experiments were conducted in a tomato greenhouse during 2005-2006 in Shouguang city, Shandong province, China. 50g/m2 MB were injected at conventional polyethylene mulching films to fumigate the soil before the tomato transplant and control received without MB. Microbial biomass C (MBC), microbial biomass N (MBN), protozoa (including three functional groups of flagellates, ciliates and amoeba), nematode (including four functional groups of bacterial-feeding nematodes, fungi-feeding nematodes, plant-parasite nematodes, omnivores-predators nematodes and the second stage juvenile of root-knot nematodes) and mites (including four functional group of predatory, omnivorous, non-cryptostigmatic, cryptostigmatic and nemaotophagous mites and the Larva and nymph mites) were compared at seven sampling times. Also, the structure of the soil food web composed with the functional groups within the unfumigated and fumigated soil was compared. The results showed that MB fumigation suppressed significantly MBC, MBN, the abundance of functional groups of flagellates, ciliates, amoebae, bacterial-feeding nematodes, fungi-feeding nematodes, plant-parasite nematodes, omnivores nematodes, the second stage juvenile of root-knot nematodes, and the total abundance of protozoa, and mites. Compared to the unfumigated soil, the MBC, MBN, total abundance of protozoa, nematode and mites decreased 45.9%、44.8%、95%、93.6% and 89.5% during the whole tomato growth stage,respectively. After soil fumigation, the number of functional groups, connectance, maximum and mean food chain length of fumigated soil food web decreased as well. It is concluded that MB fumigation decreased the abundance of each functional groups and the complexity of the soil food web structure. The MB alternative technologies that don′t affect and even promoted the soil beneficial organism were suggested.