Black cotton soil in East Africa is not a stable engineering material for highway and railroad projects. Its strong swelling potential when it absorbs water causes distresses in subgrade of highway and railroad, and thus leads to failures of the projects. This paper presents study on the swelling characteristics of black cotton soil in East Africa. Lab tests were conducted to obtain its basic engineering properties, and the results show that black cotton soil contains high amount of montmorillonite and exchangeable cations and is strong expansive soil. Molecular modelling was exploited to further investigate water absorption ability of montmorillonite. Three different molecular models of montmorillonite were constructed and used for simulations, among which Types I and II montmorillonite represent the expansive soil montmorillonite in China, and Types II and III montmorillonite represent black cotton soil montmorillonite in East Africa. The results showed that the interlayer cations of Type III montmorillonite possessed the strongest water absorption ability based on analysis of radial distribution function (RDF) of cations. Interlayer compensatory cations of Na+ enhance the hydration ability of the other major cations, thus resulting in the strong swelling potential of East-Africa black cotton soil.