A computational method utilizing divide-and-conquer and incremental computation was proposed to calculate the structure of attribute granule of an inseparable information system. Firstly, the rule that how the structure of attribute granule of an information system changed when new Functional Dependency (FD) was added to the functional dependency set of an information system was studied and the increment theorem of information system structure was proved. Secondly, by removing a part of the functional dependency, an inseparable information system could become a separable information system and the structure of the separable information system was calculated by using decomposition theorem. Thirdly, the removed functional dependency was added to the separable information system and the structure of the original information system was calculated by using increment theorem. Lastly, the algorithm to calculate the structure of attribute granule of inseparable information system was given and its complexity was analyzed. The complexity of the direct calculation of the structure of attribute granule of information system was O(n×m×2n), and the proposed method could reduce the complexity to below O(n×k×2n)(k<m), and when k=1,2, the complexity could be reduced to O(n1×m1×2n1)+O(n2×m2×2n2)(n=n1+n2,m=m1+m2). The theoretical analysis and practical calculation demonstrate that the proposed method can effectively reduce the computational complexity of the structure of attribute granule of an inseparable information system.