Ultrasonic systems are widely used for enhancing chemical, physical, and environmental processes, including particle coagulation, cavitation, and acoustophoresis. However, accurately modeling the motion of an emitter’s surface remains a challenge due to its complex interaction with surrounding media. This research addresses this issue by developing a method that considers directional displacements of all emitter surfaces in contact with the fluid across three axes. This study explores a novel approach for modeling ultrasonic emitter surface oscillations in computational fluid dynamics. The methodology involves determining natural frequencies and modal shapes using Modal analysis, followed by simulating directional surface displacements in Harmonic Acoustic analysis. The approach improves the accuracy of pressure distribution and flow field predictions by incorporating realistic boundary conditions, such as sinusoidal displacement profiles and dynamic mesh approach. These findings are validated against experimental data, confirming the model’s reliability for predicting fluid behavior under ultrasonic excitation.