Zonal water injection technique has been proved an effective method for enhanced oil recovery of multi-layer heterogeneous oil reservoirs. Higher zonal injection qualified rate is an important index for improving the effect of waterflooding development, so frequent monitoring and adjusting flowrate of separated layer is necessary. However, when traditional zonal water injection techniques are used, periodic flowrate testing and adjusting are realized by an armored cable with steel wire, which lead to a large number of testing work. This paper proposes a smart zonal water injection system based on pressure wave downhole communication technique. In this system, an integrated water distributor and a wellhead control device with pressure sensor and flow regulated assembly is developed. Continuous pressure wave can be generated by controlling the opening of downhole water distributor and wellhead control valve, and the pressure changes in wellbore can be monitored by sensors. Based on the time shift keying coding and decoding techniques, control command and downhole monitoring data are loaded into the continuous pressure wave. The pressure wave communication between wellhead control valve and downhole water distributor can be realized with injection water as the medium. With the help of General Packet Radio Service (GPRS) and Internet technology, the smart system can also be used for remote monitoring of downhole parameters and remote regulating of zonal flowrate. The smart technique for zonal water injection wells has been implemented in 89 wells in China National Petroleum Corporation (CNPC) Changqing M1 Block. Testing and adjusting work by testing vehicle in traditional zonal water injection technology is eliminated. The results of 27 tracked wells show that the maximum effective distance of pressure wave communication is 2879 m, the minimum pressure change that can be identified is 0.5 MPa, and the time of uploading a flowrate data takes 70 min. The effect of waterflooding development is improved after applying the smart technique. Zonal injection qualified rate is improved from 63.6% to 90.3%. Reservoir water absorption thickness is increased from 18.5 m to 19.4 m. Reserves producing degree of waterflooding development is improved from 68.7% to 70.2%. Natural decline rate is reduced from 5.2% to 4.8%. This paper illustrates a technology of pressure wave downhole communication for smart zonal water injection and an integrated case study, which can obtain vast amounts of real-time pressure data, and help reservoir engineers adjust development plan of waterflooding reservoirs. In addition, it offers a methodology for downhole wireless control.