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Recent research on the micro-pore structure characteristics of reservoirs during long-term water flooding in a block of the Daqing Oilfield is non-systematic and falls short on the quantitative research on the micro-pore structure parameters at different water flooding multiples. This poses a challenge for revealing the mechanism of reservoir alteration. To resolve this problem, this paper develops and presents a method, combining nuclear magnetic resonance (NMR) with mercury intrusion, to determine the value of nuclear magnetic resonance conversion coefficient (C) with corresponding changes of rock physical properties. Utilizing high pressure mercury intrusion to calibrate the pore diameter by NMR overcomes the shortcomings that the samples in the same position are unable to be reused by mercury intrusion and the conversion coefficient, C value, of NMR can not be accurately determined. By the new method the core diameter and the change of core mineral composition under different water injection multiples, the porosity and permeability of all experimental cores increase to different degrees during long-term water flooding. Long term water flooding of the core increases the pore size and lowers the clay content. Furthermore, the experiments show that kaolinite is affected most. Clay mineral variation and particle migration are the main reasons for the change of rock physical properties and pore size.