This paper presents a simple process using an SOI wafer to fabricate a silicon-based vertical microheater to generate thermal bubbles for the applications in microfluidic systems. The fabrication process consists of only two photolithography masks that provide an effective way to manufacture a resistive bulk microheater and high-aspect-ratio microchannel. The electro-thermal property of the proposed microheater has been characterized and verified by finite element analysis and experiment. According to the design concept and experimental results, the largest temperature occurred at the smallest neck section due to the non-uniform property of the resistance along the length of the arch-type microheater, and thus the vapor bubble was generated and attached on the vertical side wall of the microheater. For a typical microheater design, bubble nucleation could be generated under the applied voltage of 5V and the bubble could obstruct the entire 100 μm width of the microchannel when the applied voltage reaches 8V. A switching test has showed the silicon-based microheater has a good thermal-resistance behavior for long-term reliability and the modulation of output flow rate is easy handled by the sizes of thermal bubble. Moreover, the bubble can be formed with a steady growth even when the maximum fluid velocity is larger than 920 μm/s in a microchannel with rectangular cross-section 100 μm wide and 50 μm high. Mixing performance of the thermal bubble to disturb two collateral liquids with lamina flow was also carried out in this work. Experiments show that a high mixing efficiency could be achieved when the vapor bubble was formed in a 100 μm wide, 50 μm deep microchannel with a flow rate of 780 μm/s. These results reveal that the microfluid gate presented here is well designed and bubble sizes are stable and controllable.