Abstract It is of great importance to develop an online modeling method for chemical processes operated in closed loop for better understanding, monitoring the process or other purposes without endangering the system. This paper intends to devise an online system identification method, particularly for the batch process, by fully exploiting its intrinsic repetitiveness. It properly uses the information from the time direction and the batch direction, thus leading to a gradual performance enhancement. In addition, the identification method formulates the priori controller knowledge such as closed-loop stability as optimization constraints to refine the parameter estimates. A trust region method is employed to overcome the significant computation burden of directly handling these constraints such as solving Lyapunov inequalities. An adaptive filter is introduced to further smooth the parameter estimates. Finally, the effectiveness of the approach is verified by three numerical examples including a two-tank system.