Hydrogen (H2) is currently of strategic importance in the pursuit of a decarbonized, environmentally benign, sustainable global energy system; however, the explosive nature of H2 requires leakage monitoring to ensure safe application in industry. Therefore, H2 gas sensors with a high sensitivity and fast response across a wide concentration range are crucial yet technically challenging. In this work, we demonstrate a new type of MEMS differential thermopile gas sensor for the highly sensitive, rapid detection of trace H2 gas in air. Facilitated by a unique MIS fabrication technique, pairs of single-crystalline silicon thermopiles (i.e., sensing and reference thermopiles) are batch fabricated with high-density single-crystalline silicon thermocouples, yielding an outstanding temperature sensitivity at the sub-mK level. Such devices ensure the detection of miniscule temperature changes due to the catalytic reaction of H2 with a detection limit as low as ~1 ppm at an operating temperature of 120 °C. The MEMS differential thermopiles also exhibit a wide linear detection range (1 ppm-2%, more than four orders of magnitude) and fast response and recovery times of 1.9 s and 1.4 s, respectively, when detecting 0.1% H2 in air. Moreover, the sensors show good selectivity against common combustible gases and volatile organics, good repeatability, and long-term stability. The proposed MEMS thermopile H2 sensors hold promise for the trace detection and early warning of H2 leakage in a wide range of applications.