A side ohmic contact mode for the double channel GaN/AlGaN epitaxial layer is proposed in this paper. Rectangle transmission line model (TLM) electrodes are prepared, and the specific contact resistance is tested at the annealing temperatures from 700 °C to 850 °C. The results show that the minimum specific contact resistance is 2.58 × 10−7 Ω·cm2 at the annealing temperature of 750 °C, which is three to four times lower than the surface contact mode. Scanning electron microscope (SEM), energy dispersive spectrometer (EDS), and atomic force microscope (AFM) were carried out for the analysis of the morphology, element composition, and the height fluctuation at the contact edge. With the increase in the annealing temperature, the specific contact resistance decreases due to the alloying of electrodes and the raised number of N vacancies. However, when the annealing temperature exceeds 800 °C, the state of the stress in the electrode films transforms from compressive stress to tensile stress. Besides, the volume expansion of metal electrode film and the increase in the roughness at the contact edge leads to the degradation of the side ohmic contact characteristics.