On-chip flow cytometry provides a powerful tool to characterize cell samples for point-of-care diagnosis. In particular, sample focusing at specific locations along the microchannel is crucial to ensure the accuracy of detection. In this paper, we present a simple strategy of interfacing an RF-activated standing surface acoustic wave (SSAW) substrate with a microfluidic channel, and use this device to study the dynamic process of particle aggregation along the microchannel. Specifically, the SSAW generated by two parallel interdigital transducers induces an acoustic radiation force that propels particles suspended in the liquid toward the pressure nodes whose locations are tunable by judicious choice of the applied SSAW frequency. We also carry out a theoretical analysis that provides an estimation of the time for the particle assembly, which is validated by experimental results. This SSAW transducer can therefore be easily integrated into a microfluidic chip with moderate energy consumption, offering a convenient and effective solution in the development of on-chip flow cytometry.