Plant factory is an important field of practice in smart agriculture which uses highly sophisticated equipment for precision regulation of the environment to ensure crop growth and development efficiently. Environmental factors, such as temperature and humidity, significantly impact crop production in a plant factory. Given the inherent complexities of dynamic models associated with plant factory environments, including strong coupling, strong nonlinearity and multi-disturbances, a nonlinear adaptive decoupling control approach utilizing a high-order neural network is proposed which consists of a linear decoupling controller, a nonlinear decoupling controller and a switching function. In this paper, the parameters of the controller depend on the generalized minimum variance control rate, and an adaptive algorithm is presented to deal with uncertainties in the system. In addition, a high-order neural network is utilized to estimate the unmolded nonlinear terms, consequently mitigating the impact of nonlinearity on the system. The simulation results show that the mean error and standard error of the traditional controller for temperature control are 0.3615 and 0.8425, respectively. In contrast, the proposed control strategy has made significant improvements in both indicators, with results of 0.1655 and 0.6665, respectively. For humidity control, the mean error and standard error of the traditional controller are 0.1475 and 0.441, respectively. In comparison, the proposed control strategy has greatly improved on both indicators, with results of 0.0221 and 0.1541, respectively. The above results indicate that even under complex conditions, the proposed control strategy is capable of enabling the system to quickly track set values and enhance control performance. Overall, precise temperature and humidity control in plant factories and smart agriculture can enhance production efficiency, product quality and resource utilization.