The ordinary Portland cement concrete (OPC) has more pores and microcracks, which may cause it to suffer damages such as chlorine ion attack, and sulfate attack in a seawater environment. For optimizing the microstructure of OPC, the waterborne polyurethane modified concrete (WPMC) was prepared by adding waterborne polyurethane dispersion with relatively low-volatility and foam stabilizer based on the composition of ordinary concrete material. In addition, the test device for the capillary water absorption of concrete to investigate the properties of capillary water absorption of WPMC within 28d was designed. The results indicated that the amount of capillary water absorption of concrete was approximately linear decreased with the increase of polymer-cement ratio. The amount of capillary water absorption at 28d of WPMC with a polymer-cement ratio of 0.033 has minimum values, which was 31.03% lower than OPC. The addition of waterborne polyurethane dispersion can refine the internal pore structure of concrete, improving the density of concrete, and reducing the capillary water absorption of concrete.