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Rough set theory as a mathematic method can be used to mine the latent rules of dynamic information system. Generally, the results of rules mining using this method are not satisfying due to inconsistence of information system and uncertainty and difference in the process of construction of dynamic information system. An approach to eliminate the cause of inconsistence of rules mining in difference information system is presented under the background of covering theory. Experiment shows that relationship between the changes of condition attributes values and trend of decision-making can be fully reflected as much as possible through this pre-process approach by a modified rules mining algorithm.