As a supplementary method to single crystal X-ray diffraction (XRD), nowadays crystal structure determination by powder XRD has become popular, especially for those areas with difficulties getting high quality single crystals. Here we observed an intermediate phase Bi(2)Mn(x)Al(7-x)O(14) (x~1) during the decomposition of mullite-Bi(2)Mn(x)Al(4-x)O(9+δ) (solid solution of Bi(2)Mn(4)O(10)-Bi(2)Al(4)O(9)). As a metastable phase, it started to decompose while forming, thus no single-phase sample can be obtained. We successfully determined its structure by powder XRD from a multi-phase sample. A modified Le Bail fitting using the atomic structure information of known impurities showed a more reliable intensity extraction from a multi-phase powder XRD than that without using atomic structures for the known impurities. The charge-flipping algorithm and Monte-Carlo based simulated annealing technique were then applied to obtain the full structural model. In principle, this strategy is applicable to more complex problems, and not limited to the oxide materials. Bi(2)Mn(x)Al(7-x)O(14) possesses a mullite-related structure. There are one tetrahedral and two octahedral sites for Mn and Al, where disordering with substantial site preferences is observed. Specifically, M1O(6) and M3O(6) octahedra share edges along the c-direction with the periodicity of 1 : 2. These octahedral chains are further connected into a 3D structure through M2O(4) dimmers and Bi.