A two-year field study with split plot design was conducted to investigate the effects of different soil tillage (conventional tillage, CT; deep tillage, DT; subsoil tillage, ST) and straw returning (all straw retention, AS; no straw returning, NS) on microorganism quantity, enzyme activities in soil and grain yield. The results showed that, deep or subsoil tillage and straw returning not only reduced the soil bulk density and promoted the content of organic carbon in soil, but increased the soil microbial quantity, soil enzyme activities and grain yield. Furthermore, such influences in maize season were greater than that in wheat season. Compared with CT+NS, DT+AS and ST+AS decreased the soil bulk density at 20-30 cm depth by 8.5% and 6.6%, increased the content of soil organic carbon by 14.8% and 12.4%, increased the microorganism quantity by 45.9% and 33.9%, increased the soil enzyme activities by 34.1% and 25.5%, increased the grain yield by 18.0% and 19.3%, respectively. No significant difference was observed between DT+AS and ST+AS. We concluded that retaining crop residue and deep or subsoil tillage improved soil microorganism quantity, enzyme activities and crop yield.