Standing surface acoustic waves (SSAWs) have been extensively used as acoustic tweezers to manipulate, transport, and separate microparticles and biological cells in a microscale fluidic environment, with great potentials for biomedical sensing, genetic analysis, and therapeutics applications. Currently, there lacks an accurate, reliable, and efficient three-dimensional (3D) modeling platform to simulate behaviors of micron-size particles/cells in acoustofluidics, which is crucial to provide the guidance for the experimental studies. The major challenge for achieving this is the computational complexity of 3D modeling. Herein, a simplified but effective 3D SSAW microfluidic model was developed to investigate the separation and manipulation of particles. This model incorporates propagation attenuation of the surface waves to increase the modeling accuracy, while simplifies the modeling of piezoelectric substrates and the wall of microchannel by determining the effective propagation region of the substrate. We have simulated the SSAWs microfluidics device, and systematically analyzed effects of voltage, tilt angle, and flow rate on the separation of the particles under the SSAWs. The obtained simulation results are compared with those obtained from the experimental studies, showing good agreements. This simplified modeling platform could become a convenient tool for acoustofluidic research.