Summary: It is pretty significant for fault diagnosis timely and accurately to improve the dependability of industrial processes. In this study, fault diagnosis of nonlinear and large-scale processes by variable-weighted Kernel Fisher Discriminant Analysis (KFDA) based on Improved Biogeography-Based Optimisation (IBBO) is proposed, referred to as IBBO-KFDA, where IBBO is used to determine the parameters of variable-weighted KFDA, and variable-weighted KFDA is used to solve the multi-classification overlapping problem. The main contributions of this work are fourfold to further improve the performance of KFDA for fault diagnosis. First, a nonlinear fault diagnosis approach with variable-weighted KFDA is developed for maximizing separation between the overlapping fault samples. Second, kernel parameters and features selection of variable-weighted KFDA are simultaneously optimized using IBBO. Finally, a single fitness function that combines erroneous diagnosis rate with feature cost is created, a novel mixed kernel function is introduced to improve the classification capability in the feature space and diagnosis accuracy of the IBBO-KFDA, and serves as the target function in the optimization problem. Moreover, an IBBO approach is developed to obtain the better quality of solution and faster convergence speed. On the one hand, the proposed IBBO-KFDA method is first used on Tennessee Eastman process benchmark data sets to validate the feasibility and efficiency. On the other hand, IBBO-KFDA is applied to diagnose faults of automation gauge control system. Simulation results demonstrate that IBBO-KFDA can obtain better kernel parameters and feature vectors with a lower computing cost, higher diagnosis accuracy and a better real-time capacity.