The investigation of aluminum gallium nitride/gallium nitride high electron mobility transistor (AlGaN/GaN HEMT) devices with a dual‐metal gate (DMG) structure encompasses both electrical and thermal characteristics. As efforts to enhance heat dissipation progress, there is a concurrent exploration of novel semiconductor materials boasting high thermal conductivity, like boron arsenide and phosphide. Combining these materials into a model and measuring their interface achieves efficient energy transport. Minimizing the self‐heating impact in AlGaN/GaN HEMTs is essential for enhancing device efficiency. This research exposes the heterogenous combination of boron arsenide and phosphide cooling substrates with metals, GaN semiconductors and HEMT. In this research, the autoencoder deep neural network techniques in GaN HEMT for self‐heat reduction is driven by the ability to effectively analyze and model the thermal behavior of the device. Autoencoders learn complex relationships within temperature data and identify patterns associated with self‐heating. By leveraging these learned representations, the deep neural network optimizes control strategies to mitigate self‐heating effects in GaN HEMT devices, ultimately contributing to improved thermal management and enhanced overall performance. In this research, the use of genetic algorithms in GaN HEMT aims to optimize device parameters systematically, to minimize self‐heating effects and enhance overall thermal performance. The structure also enhances electron mobility within the channel. Results show DMG structures, exhibiting higher saturation output currents and transconductance despite self‐heating. The DMG exhibits a maximum gm value of 0.164 S/mm, which is 10% higher significantly enhancing GaN‐based HEMTs for improved reliability and efficiency in various applications.