The rational manufacturing of multi-component materials with rich heterostructure is emerging as a possible strategy to develop improved carbon nanotube-based gas sensors. Herein, hierarchical heterostructure of multiwalled carbon nanotubes/SnO2 nanorod-flowers (HMCNS) was synthesized by a facile water-bathing combined hydrothermal approach for highly sensitive ammonia detection. Exploration in the microstructure reveals that hierarchical flowers-like SnO2 consisted of nanorods demonstrates a hollow geometry for wrapping multiwalled carbon nanotubes, featuring a unique three-dimensional (3D) hierarchical architecture. Gas sensor based on SnO2@4.5%CNTs hierarchical heterostructure exhibits highly enhanced ammonia-sensing performances, including ultra-high response of 1650 toward 20 ppm ammonia, good selectivity, 250 ppb level detection, and superior long-term stability. The improvement in ammonia sensing capability could be attributed to the peculiar hierarchical architecture and the creation of Mott-Schottky heterostructure which has been strongly validated by electrochemical research. This work will provide a concise and effective avenue to construct hierarchical composite with Mott-Schottky heterostructure for high-performance ammonia gas sensor.