Due to the complex conditions of carbonate reservoir, in this paper, a unified lattice Boltzmann method was used to study the rule of the flow in carbonate reservoir as the foundation. Two group models were designed to simulate the influences of fractures and vugs. In experiments, at first, the model for carbonate reservoir considering different amounts and lengths of fractures was considered. Then, the model was improved by taking the influences of fractures and vugs into consideration. The result from the first group shows that the whole permeability enhanced a lot when multiple fractures form a big one which connects to two boundaries. At the same time, the main result of the other group shows that the main capability of vugs is flow accumulation. Through a series of experiments, the flow rule in carbonate reservoir with vugs and fractures is proved based on LBM theory, which has a huge impact on the study in LBM and researches on carbonate reservoir.