Yield increases of cucumber following cover crops in a rotation system have been previously reported for intensive Chinese agricultural production. However, little information is available as to how this system affects soil microbial properties and nematodes. A 4-year field experiment on a greenhouse cucumber double-cropping system was conducted to investigate the effects of four different summer cover crops on cucumber yield, soil nutrients, microbial properties and nematodes. After 4 years, six cover crop and residue management rotational cropping systems that included sweet corn residue removed (SR), sweet corn residue incorporated (SI), and garland chrysanthemum and edible amaranth (GR) significantly (P < 0.05) increased cucumber fruit yields summed for the years 2005–2008 by 22%, 32% and 26%, compared to the control (CONTROL), while cropping systems that included common bean residue removed (CR) and common bean residue incorporated (CI) significantly (P < 0.05) decreased yields by 30% and 22%, respectively. Plant available N losses and P, K accumulation in soil were efficiently reduced by planting cover crops. Soil microbial biomass, population and diversity were higher under summer cover crop-related treatments than under the control. The dominant plant-parasitic nematodes found in our experiment field were Meloidogyne sp. and Helicotylenchus sp, which were all parasites of both common bean and cucumber. A strong relationship between cucumber yields and the non-plant-parasitic: plant-parasitic nematode ratio (NPR) (r = 0.703, p < 0.001) was found in the break-host systems (SR, SI and GR). These results suggested that on the nutrient rich soils of our study, cucumber yield increases for the SR, SI and GR treatments, compared with the control, could be explained by higher microbial biomass, population and diversity and NPR.