Given the complex characteristics of permanent magnet linear synchronous motors and the external interference encountered during their operation, controlled precision and efficiency are necessary. In this paper, the mechanism of biological endocrine hormone regulation is analyzed, and an intelligent controller based on the obtained neuroendocrine algorithm is implemented in the control system of a permanent magnet linear synchronous motor. The controller mainly includes a hypothalamic regulation module, a single-neuron proportion integration differential module, and an ultrashort feedback module. It is designed and referenced to the long feedback, short feedback, and ultrashort feedback loop mechanisms of neuroendocrine hormone regulation and abides by the principle of human neuroendocrine hormone regulation. The antagonistic hormone regulation module achieves rapid and stable elimination of errors through the fusion of enhanced regulation with regulation inhibition, and the single-neuron proportion integration differential module enhances the adaptive and self-learning capabilities of the control system. The proposed control is successfully used in a permanent magnet linear synchronous motor, and the experimental results show that the controller presents many advantages, such as fast dynamic responses, strong online adjustment ability, and good running stability in the control system, all of which improve the robustness of the control system.