Large-scale three-dimensional ultrasonic vibration systems are susceptible to the influence of coupled vibration, resulting in a series of problems such as increased energy loss, small longitudinal displacement amplitude of the radiation surface, and uneven distribution of longitudinal displacement amplitude, which can seriously affect the working efficiency of ultrasonic processing system. How to effectively control the coupled vibration of large-scale three-dimensional ultrasonic transducer systems and optimize their performance has become an urgent problem in the field of power ultrasound. The research has found that some phononic crystal slots and point defect structures can suppress the lateral vibration of large-scale transducer systems, improve the uniformity of system amplitude distribution, and artificially regulate the performance of large-scale three-dimensional ultrasonic vibration systems by changing the configuration parameters of phononic crystal structures. However, excessive design parameters will inevitably increase the complexity of system design, and, currently, the optimization design of large-scale three-dimensional ultrasonic transducer systems relies on empirical trial and error methods which has low design efficiency and low success rate, and cannot guarantee the system performance. Therefore, in the study, homogeneous dislocations and point defect structures are introduced to optimize the design of large-scale three-dimensional ultrasonic vibration systems. Data analysis techniques are used to evaluate the influences of the configuration of homogeneous dislocations and point defect structures on the longitudinal displacement amplitude, amplitude distribution uniformity, radiated sound power, working bandwidth of the system’s radiation surface. And a predictive model for the performance of large-scale ultrasonic transducer system with homogeneous dislocation structure and near periodic defect structure is established, which can achieve intelligent design of large-scale power ultrasonic transducer system, improve design efficiency and success rate, and reduce the design cost.