In order to provide more accurate information for decisions of managers, the input-output theory is introduced into enterprise management information system to effectively solve cost accounting problems. Through the analysis of a variety of traditional cost accounting methods, using input-output analysis, the weighted average method and Gauss-Seidel iterative, we establish a model of product costing, and design the accurate and efficient algorithms. This cost model and algorithm based on input-output theory, not only has overcome the shortcomings of traditional cost accounting, fully meets the accounting requirements, simultaneously can provide systematic and comprehensive data for enterprise management, and has achieved "cost accounting" and "enterprise management" the organic unification.