Measurements of thermal boundary resistance (TBR) are of great significance in the fields of electronic packaging and thermal management. In this study, a measurement method based on a designed 1 × 1 mm2 chip with a heat source separated from a temperature sensor was developed. The chip consists of a temperature sensor with nine Schottky diodes connected in series and a heat source composed of metal wires, which are separated by SiO2 to realize electrical isolation. With this chip, the TBR of samples can be extracted from transient temperature response curves of GaN on a Si wafer using the structure function and transient dual interface test methods. In particular, the surface of samples was etched with uniform arrays to increase the measurement accuracy. The TBR measurements of four samples etched on the same wafer under different conditions were 1.62 ± 0.22 × 10−8, 1.6 ± 0.38 × 10−8, 1.49 ± 0.18 × 10−8, and 1.6 ± 0.35 × 10−8 m2K/W, indicating consistency of the results. This chip effectively expands the application of the structure function method to TBR measurements, which can be helpful for further research on interfacial heat transport.