Two long-term field experiments, each consisting of three treatments (organic compost treatment, chemical fertilizer treatment and an untreated control) were established in 1993 and 1997, respectively. Soil samples were collected from each plot in June 2004 and 2005 after crop harvest and were used to determine soil physical-chemical properties, biological and biochemical activity, and the nematode community. Soil physicochemical parameters, microbial biomass, biological activities and nematode communities were significantly influenced by long-term application of organic compost. In general, soil total organic carbon, dissolved organic carbon, total nitrogen, alkaline-hydrolysable nitrogen, available phosphorus, and available potassium, microbial biomass, basal respiration, urease activities, total number of nematodes and bacterial-feeding nematodes were significantly higher in the compost plots than in the chemical fertilizer and control plots at two experimental sites and two sampling dates. Soil bulk density and pH values were significantly lower in the compost plots. We conclude that soil physical-chemical properties, size and activity of soil microbial biomass, metabolic quotient (qCO2), urease activity, total number of nematodes and bacteria-feeding nematodes could be used as indicators of soil quality.