In order to investigate the influence of different barnyardgrass species on rice yield and physiological characteristics of rice, two rice cultivars, Liangyoupeijiu (an indica hybrid cultivar) and Nanjing 9108 (a japonica cultivar), were employed to coculture with four barnyardgrass species during the period from transplanting to maturity under alternate wetting and moderate drying irrigation condition. The treatments were separately designed as follow: weed free (control), rice with Echinochloa crusgalli var. mitis (T₁), rice with E. crusgalli (T₂), rice with E. crusgali var. zelayensis (T₃) and rice with E. colonum (T₄). The results showed that T₁, T₂,T₃ and T₄ treatments reduced the Liangyoupeijiu yield by 13.8%, 10.6%, 23.8% and 0.5%, but the corresponding yield loss of Nanjing 9108 could reach up to 45.5%, 36.9%, 60.7% and 15.1%, respectively. The results above showed that T₁, T₂ and T₃ treatments all significantly reduced grain yield, and T₄ treatment only reduced grain yield for Nanjing 9108 but not for Liangyoupeijiu. All treatments  elevated malondialehyde contents of rice leaf, but the activities of peroxidase, catalase, superoxide dimutase, dry matter accumulation in maturity stage, root oxidation activities and contents of indole-3-acetic acid as well as zeatin+zeatin riboside in roots during rice grain filling stage were all decreased. The influence degree of four barnyardgrass against physiological indices of rice had the order of T₃>T₁>T₂>T₄. It showed that the reductions in  enzyme activities of antioxidant system, root oxidation activities, contents of indole-3-acetic acid, zeatin+zeatin riboside during grain filling stage and accumulation of dry matter in maturity as well as increase in contents of malondialehyde of rice during grain filling stage might be important reasons for grain yield reduction when grew with barnyardgrass.