PurposeThe flexibility of batch process enables its wide application in fine-chemical, pharmaceutical and semi-conductor industries, whilst its complexity necessitates control performance monitoring to ensure high operation efficiency. This paper proposes a data-driven approach to carry out controller performance monitoring within batch based on linear quadratic Gaussian (LQG) method.Design/methodology/approachA linear time-varying LQG method is proposed to obtain the joint covariance benchmark for the stochastic part of batch process input/output. From historical golden operation batch, linear time-varying (LTV) system and noise models are identified based on generalized observer Markov parameters realization.FindingsOpen/closed loop input and output data are applied to identify the process model as well as the disturbance model, both in Markov parameter form. Then the optimal covariance of joint input and output can be obtained by the LQG method. The Hotelling's Tˆ2 control chart can be established to monitor the controller.Originality/value(1) An observer Markov parameter approach to identify the time-varying process and noise models from both open and closed loop data, (2) a linear time-varying LQG optimal control law to obtain the optimal benchmark covariance of joint input and output and (3) a joint input and output multivariate control chart based on Hotelling's T2 statistic for controller performance monitoring.