The East African Rift System, as the most famous continental rift and fault zone on earth, conducting research on the formation of ground fissures within the rift valley is of great significance for understanding the active rift process and guiding the engineering construction of the rift valley area. On the basis of field investigation, trenching, geophysical exploration, and helium isotope detection of ground fissures in the Kenya Rift Valley, East Africa, this article establishes a multi-level structure of ground fissures in the crust and analyzes their formation mechanisms. The results indicate that there are a total of 22 large ground fissures developed in the study area, mainly distributed in the rift basin between the eastern boundary fault and two volcanoes in the study area. Ground fissures appear on the surface as ruptures and collapses of loose sediments, and as simple tensile fractures with degassing on the surface of pyroclastic rocks. Resistivity detection shows that ground fissures are extensions of rock fissures in the crust. Based on the characteristics of helium isotopes, a multi-level structure consisting of ground fissures, rock fractures, faults, magma chambers, faults, and upper mantle has been revealed. On the basis of the above research, combined with the characteristics of crustal deformation and numerical simulation, the formation mechanism of ground fissures in Kenya Rift Valley, was revealed and summarized as follows: mantle upwelling-mantle intrusion-magma chamber expansion-surface fracturing.