Chemical reaction systems are often complex dynamic time-delay systems that have to operate successfully in the presence of uncertainties. Under these circumstances, flexibility analysis comes to be much important to the design and operation of time-delay chemical reaction systems. In this work, a modified finite element collocation method was proposed to carry out flexibility analysis of chemical reaction systems with time delay. The proposed method is combined with the linear quadratic regulator (LQR) and Lagrange polynomial for the optimal solution of control variables and state variables respectively. The method is investigated by two typical chemical reaction systems with time delay. All the results demonstrate that the proposed modified finite element collocation method may provide a powerful tool for studying the dynamic flexibility of chemical reaction systems with time delay. (C) 2011 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.