The fuzzy probability rough set over two universes is a new data mining model for the two universes information system. However, the two universes information system in real application is always in dynamic updating. In order to solve this problem, a fuzzy probability rough set over two universes incremental updating method based on the matrix is proposed. Firstly, the fuzzy probability rough sets over two universes are expressed by matrix method. Then, on the basis of matrix expression model, the incremental updating mechanism of the model is studied when the objects increase and decrease in two universes of the two universes information system, respectively. And based on this incremental updating, the corresponding incremental updating algorithm is finally proposed. The experimental analysis shows that the proposed incremental updating algorithm can complete dynamic updating of the model in a very short time compared to the non-incremental updating algorithm, which verifies the effectiveness of the proposed algorithm. At the same time, compared with other related algorithms, the proposed algorithm has certain advantages.