Temperature control within a microreactor is critical for biochemical and biomedical applications. Recently acoustothermal heating using surface acoustic wave (SAW) devices made of bulk LiNbO3 substrates have been demonstrated. However, these are generally fragile and difficult to be integrated into a single lab-on-a-chip. In this paper, we propose a rapid and controllable acoustothermal microheater using AlN/Si thin film SAWs. The device’s acoustothermal heating characteristics have been investigated and are superior to other types of thin film SAW devices (e.g., ZnO/Al and ZnO/Si). The dynamic heating processes of AlN/Si SAW devices for both a sessile droplet and liquid within a polydimethylsiloxane (PDMS) microchamber were characterized. Results show that for the sessile droplet heating, the temperature at a high RF power is unstable due to significant droplet deformation and vibration, whereas for the liquid within the microchamber, the temperature can be precisely controlled by the input power with good stability and repeatability. In addition, an improved temperature uniformity using the standing SAW heating was demonstrated as compared to that of the travelling SAWs. Our work shows that the AlN/Si thin film SAWs have a great potential for applications in microfluidic heating such as accelerating biochemical reactions and DNA amplification.