In the past decades, on-line monitoring of batch processes using multi-way independent component analysis (MICA) has received considerable attention in both academia and industry. This paper focuses on two troublesome issues concerning selecting dominant independent components without a standard criterion and determining the control limits of monitoring statistics in the presence of non-Gaussian distribution. To optimize the number of key independent components, we introduce a novel concept of system deviation, which is able to evaluate the reconstructed observations with different independent components. The monitored statistics are transformed to Gaussian distribution data by means of Box-Cox transformation, which helps readily determine the control limits. The proposed method is applied to on-line monitoring of a fed-batch penicillin fermentation simulator, and the experimental results indicate the advantages of the improved MICA monitoring compared to the conventional methods.