A heat exchanger controlled by manipulating flow rates is widely used and there often exist unknown disturbance flows in the system. If we approximate the distributed parameter system to a lumped parameter system by means of Method of Weighted Residuals (MWR) and apply a controller to depress the disturbance influence, we must take the following three points into account: (a) the system has bilinear terms with respect to not only the input but also the unknown disturbance, (b) we cannot observe the state vector directly because the components are generalized Fourier coefficients so they are not physical quantities, and (c) we must rely on estimators to obtain the internal temperature accurately due to the heat exchanger structure. In this paper, we consider H ∞ control problems for such a bilinear system and design a bilinear H ∞ controller using a bilinear observer. As a bilinear observer, we use "a bilinear disturbance isolation observer (DIO)" which is an extension of a previous work. The performance of this observer-based H ∞ controller is evaluated with several simulations and experiments.