A hierarchical control scheme for the time-optimal operation of a semibatch emulsion polymerization reactor using a new technique to calculate the set points of the molar holdups of the reactants is presented and validated by simulations of a rigorous process model. The goal is to produce polymer with a desired molecular weight distribution by emulsion polymerization using a CTA. The novelty of the proposed hierarchical control scheme is that limiting constraints are identified at which the process is operated at its maximum propagation reaction rate. These boundaries result from the avoidance of the formation of a droplet phase and the limited heat removal capacity, the latter of which is an extremely important consideration for larger reactors. To drive the process at its maximum heat removal capacity, a reliable estimation of the heat-transfer coefficient is needed. In the control scheme presented here, a state estimator is used that estimates the heat of reaction and the heat-transfer coefficient of the cooling jacket. Our focus is on the control of pilot-scale and industrial-size reactors; therefore the fact that, for large reactors, the cooling jacket behaves not like an ideal continuously stirred tank reactor (CSTR) but rather like a plug-flow reactor (PFR) must be taken into account. A discretized PDE model of the jacket is used in the estimation scheme. The estimate of the heat of reaction is fed to a simulation model to estimate the amounts of monomer and of CTA in the reactor. The ratio of these two quantities is compared with the required ratio needed to obtain the desired molecular weight distribution, which is calculated off-line. The amount of monomer in the reactor determines the reaction rate, the ratio determines the molecular weight of the polymer obtained. When the process is driven along the constraints, decentralized linear controllers are sufficient to achieve good control performance and to obtain the desired molecular weight distribution.