Acoustic trap, using ultrasound interference to ensnare bioparticles, has emerged as a versatile tool for life sciences due to its non-invasive nature. Bolstered by magnetic resonance imaging’s advances in sensing acoustic interference and tracking drug carriers (e.g., microbubble), acoustic trap holds promise for increasing MRI-guided microbubbles (MBs) accumulation in target microvessels, improving drug carrier concentration. However, accurate trap generation remains challenging due to complex ultrasound propagation in tissues. Moreover, the MBs’ short lifetime demands high computation efficiency for trap position adjustments based on real-time MRI-guided carrier monitoring. To this end, we propose a machine learning-based model to modulate the transducer array. Our model delivers accurate prediction of both time-of-flight (ToF) and pressure amplitude, achieving low average prediction errors for ToF (−0.45 µs to 0.67 µs, with only a few isolated outliers) and amplitude (−0.34% to 1.75%). Compared with the existing methods, our model enables rapid prediction (<10 ms), achieving a four-order of magnitude improvement in computational efficiency. Validation results based on different transducer sizes and penetration depths support the model’s adaptability and potential for future ultrasound treatments.