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Abstract Power intensification and miniaturization of electronics and energy systems are causing a critical challenge for thermal management. Single-phase heat transfer mechanisms including natural and forced convection of air and liquids cannot meet the ever-increasing demands. Two-phase heat transfer modes, such as evaporation, pool boiling, flow boiling, have much higher cooling capacities but are limited by a variety of practical instabilities, e.g., the critical heat flux (CHF), aka departure from nucleate boiling (DNB) in the nuclear industry, flow maldistribution, flow reversal, among others. These instabilities are often triggered suddenly during normal operation, and if not identified and mitigated in time, will lead to overheating issues and detrimental device failures. For example, when CHF is triggered during pool boiling, the device temperature can ramp up in the order of 150 °C/min. It is thus critical to implement real-time detection and mitigation algorithms for two-phase cooling. In the present work, we have developed an accurate and reliable technology for fault detection of high-performance two-phase cooling systems by coupling acoustic emission (AE) with multimodal fusion using deep learning. We have leveraged the contact AE sensor attached to the heater and hydrophones immersed in the working fluid to enable non-invasive fault detection.