The invention relates to a method and system for establishing a multilayer oil pool inter-well connectivity model. The multilayer oil pool inter-well connectivity model capable of simulating oil and water dynamic states is established oriented to the limitation that by means of a current connectivity model, only the dynamic change of production liquid can be predicted, the dynamic states of the oil phase and the water phase cannot be calculated respectively, and connectivity analysis cannot be carried out layer by layer. According to the model, an oil pool system is layered and scattered into a series of inter-well communication units, matter balance equation calculation is carried out with the inter-well communication units as simulating objects, pressure solving and inter-well flow calculation are achieved, an inter-well saturation degree tracking calculating method is established with the combination of the lead edge boosting theory, and the output dynamic states of oil and water of all layers at well points are obtained; a model parameter inversion method is established in a fitting mode through dynamic states based on a random disturbance approximation method, a projection gradient method and the like. Layered inter-well flow distribution coefficients, single well longitudinal production liquid and production oil splitting coefficients and other information can be obtained in real time, the oil pool plane, the longitudinal oil and water flow relation and the production measure change can be more accurately reflected to guide the practical production of an oil field.