Due to increased complexity and interactions between various subsystems, higher-order MIMO systems present difficulties in terms of stability and control performance. This study effort provides a novel, all-encompassing method for creating a decentralized fractional-order control technique for higher-order systems. Given the greater number of variables that needed to be optimized for fractional order control in higher-order, multi-input, multi-output systems, the modified flower pollination optimization algorithm (MFPOA) optimization technique was chosen due to its rapid convergence speed and minimal computational effort. The goal of the design is to improve control performance. Maximum overshoot (Mp), rising time (tr), and settling time (ts) are the performance factors taken into consideration. The MFPOA approach is used to improve the settings of the proposed decentralized fractional-order proportional-integral-derivative (FOPID) controller. By exploring the parameter space and converging on the best controller settings, the MFPOA examines the parameter space and satisfies the imposed constraints by maintaining system stability. To evaluate the suggested approach, simulation studies on two systems are carried out. The results show that by decreasing the loop interactions between subsystems with improved stability, the decentralized control with the MFPOA-based FOPID controller provides better control performance.