In this paper we present a new state space model based linear quadratic fault-tolerant tracking control scheme for batch processes with unknown disturbances and partial actuator faults. To develop the linear quadratic fault-tolerant control, the batch process is first treated with a new state space representation that incorporates both the state and the output tracking error dynamics. Then relevant concepts of the subsequent linear quadratic control are formulated, where improved closed-loop control performance is achieved even with unknown disturbances and actuator faults compared with traditional linear quadratic control. Application to injection velocity control shows that the proposed scheme achieves the design objective well with performance improvement.