Waterflood is one of the main oil reservoir development ways. Premature flooding of production wells during water flooding process will reduce oil recovery. Therefore，it is particularly important to establish a dynamic tracking model for reservoir water flooding of separated zone water injection. Based on the basic principles of heat and mass transfer，according to well temperature curve to determine the water profile，Poisson process analysis and stochastic process methods are adopted to calculate water saturation，water breakthrough time and water cut of each layer in water flooded reservoir at any one time. When oil reservoir gradually become water flooded，the calculated water cut of model considering micro-pore distribution of the reservoir tends to the measured water cut，and the calculation error is less than 5%. Case study shows that the layer of the higher injection rate，with high flow channel such as micro fracture，where there is the faster increase in water saturation，the shorter water breakthrough time and faster increase in water cut，and vice versa. Research result provides time guarantee to take measures for inhibiting or delaying water breakthrough of production wells.