Abstract The biolithite reservoir has a strong heterogeneity and complex pore structure, and the changing trend of formation resistivity is complicated during the waterflood development process. In the logging interpretation of a water-flooded layer, mixed-formation water resistivity is a critical parameter and its accurate calculation heavily influences the evaluation of logging water saturation. The commonly used mixed liquid resistivity models have not taken into account the contribution of irreducible clay water and, thus, they are not suitable for biolithite reservoirs with high shale contents. In this paper, a new 3D digital core was constructed based on CT scanning, and a progressive ion exchange model of the mixed-formation water compatible with the biolithite reservoir put forward. Compared with experimental data from core water flooding, the progressive ion exchange model conforms to the resistivity change law of biolithite reservoirs. Through numerical simulation and analysis of the resistivity of biolithite reservoir, it is concluded that the salinity of injected water and the formation water saturation are the main factors affecting the resistivity characteristics of water-flooded layer. In terms of the interpretation of the water-flooded layer, the water saturation was calculated using the progressive ion exchange model through finite element modelling of formation resistivity. The particular mechanism of water flooding and changing law of rock electrical properties during reservoir water injection development are presented, which provide a new reliable basis for optimization of the biolithite reservoir development plan.