Among the existing algorithms of data classification in material balance systems, the zeromatrix method has many advantages, such as simplicity in construction and high efficiency. However, it can′t classify data thoroughly. It will affect the performance and reliability of material balance systems. To overcome these problems, the paper proposes an improved zeromatrix algorithm which introduces the notion of absolute maximum linear independent column in the preprocessing stage of data classification. Through repartitioning the matrix, the new algorithm can classify the data thoroughly. The numerical experiment shows that the algorithm improves the accuracy and performance of the material balance system.