To obtain environmentally friendly, integrated and miniaturized gas sensors for the increasing request for the Internet of Things industry and other relative areas, the ultra-thin CoOx/ZnO heterogeneous film with active interfacial sites was in-situ deposited on micro-electro-mechanical systems (MEMS) as H2S sensor. Atomic layer deposition (ALD) was employed to in-situ fabricate the uniform ZnO thin film. ALD CoOx was deposited on ZnO surface to obtain CoOx/ZnO heterojunction and active interfacial sites. The ultra-thin film (20 nm) with 50 ALD CoOx decorated on 250 ALD ZnO displays excellent sensing performance, including very high response (4.45@200 × 10−9) and selectivity to H2S with a limit of detection (LOD) of 0.38 × 10−9, long-term sensing stability, high response/recovery performance (7.5 s/15.7 s) and mechanical strength at 230 °C. Reasons for the high sensing performance of CoOx/ZnO have been confirmed by series of characterizations and density functional theory (DFT) calculation. Heterojunction film thickness with Debye length, the oxygen vacancies and the synergistic effect of active interfacial sites are main reasons for the high sensing performance. The strategy by fabrication of CoOx/ZnO heterogeneous film within Debye length and employing synergistic effect of active interfacial sites offers a promising route for the design of environmentally friendly gas sensors. Furthermore, the ALD technique offers a facile in-situ strategy and high-throughput fabrication of MEMS gas sensors.Graphical Abstract