This experiment was conducted at Sinheung series (fine loamy, mixed, nonacid, mesic family of Fluvaquentic Endoaquepts) in 2007 to 2008 at the National Institute of Crop Science (NICS), RDA, Suwon, Gyeonggi province, Korea. Three kinds of green manure crops (hairy vetch, barley, rye) incorporated in soil for rice cultivation. 6.3 kg N $10a^{-1}$, and3.2 kg $P_2O_5$ $10a^{-1}$ were applied to rye and barley plot before rice transplanting. Chemical fertilizers had not been applied to hairy vetch plot. Glomalin concentration, soil bulk density, and porosity were measured in soil from different green manure crops incorporation after rice harvesting in paddy. Soil bulk density and porosity after rice harvesting improved at surface soil of hairy vetch incorporation plot. Degree of water stable aggregates increased all green manure incorporation plots. Glomalin concentrations significantly increased at hairy vetch incorporation treatment. In barley plot, the concentration of glomalin increased at 10-20 soil depth. There were no differences relationship between soil carbon, and glomalin concentration, but relationship between soil aggregate stability, and glomalin concentration significantly positive under green manure crop-rice cropping system. Rice yield decreased at hairy vetch incorporation plot because of field lodging. We suggested that hairy vetch incorporation should be considered about application amount, and water management using rice cultivation because of soil properties changes.