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This paper proposes an integration system to the logistics enterprise information system in distributed heterogeneous environment. We establish a framework structure of universal data mining system based on logistics data warehouse and apply the proposed system into practical management of logistics and shipping enterprises. Feature extraction and data sample classification from large-scale data warehouse is realized by constructing the logical feature space and generating the rule and pattern about the logical feature sub-space, which can help data mining system earn necessary knowledge about a specific part of a real or abstract information and further use the knowledge to match data mining models. The discussed results of illustrative example and numerical simulation show that the developed models system and methodologies can be useful and applicable to realize the intelligent decision support system in the logistics enterprise and supply chain management.