Most thin interbed reservoirs face a common problem that a nonequilibrium injection and production relationship in plane and vertical directions results in quick water breakthrough, rapid water-cut rise, and a poor water flooding efficiency in a single layer. A finer injection-production strategy should be developed to avoid serious water channeling and an ineffective water cycle. To narrow this gap, this work presents a three-dimensional intelligent equilibrium displacement model (3D-IEDM) to optimize water flooding in thin interbed reservoirs. A water-injection splitting model is first established to determine the water-injection rate of each layer based on displacement pressure and flow resistance. Then, water saturation is calculated for the injection-production well group based on the material balance principle. To achieve three-dimensional equilibrium flooding, the minimum water saturation variance is chosen as the optimization target and the improved particle swarm optimization algorithm is employed to reduce the optimization time caused by iterative calculations. Finally, the 3D-IEDM is programmed as software to provide a quantitative equilibrium flooding optimization scheme in an actual oilfield. The implementation in the pilot B36 well group test of the PL oilfield indicates that the optimization velocity of the 3D-IEDM can optimize the vertical water injection profile of thin interbed reservoirs and improve the sweep efficiency, and the length of time is approximately 14 times less than that of conventional simulator-based methods. Compared with the conventional injection-production scheme, the initial productivity of the pilot well group using the 3D-IEDM increases by 6.45%, and the utilization factor of water injection improves by 15%.