The invention relates to a computed tomography (CT) scanning heterogeneous model testing system. The system comprises a CT scanning system, a displacement system, an overburden pressure system, a pressure measurement system, a heterogeneous multilayer core clamp holder and a metering system, wherein the heterogeneous multilayer core clamp holder consists of a shell, a rubber cylinder, a core left plug, a core right plug, a left fixing sleeve, a right fixing sleeve, a left fastening sleeve, a right fastening sleeve and a fixed bracket; the core right plug is provided with a plurality of liquid outlets; each liquid outlet is respectively aligned with one layer of core model; and a strip liquid outlet sealing gasket is formed on the core right plug, which correspond to a seam between two adjacent layers of core models, so that liquid flow passing through each layer of core model flows out from the corresponding liquid outlet of each layer of core model, and thus, intraformational heterogeneous water displacing oil layered measurement is realized. By the CT scanning system, the real-time on-line monitoring of the on-way distribution of saturation of fluid on each layer section in a heterosphere is realized so as to observe the interlayer communication phenomenon.