The environmental control of layer houses with multi-tiered cage systems is influenced by factors such as the structure of the henhouses and the heat dissipation of the flock, leading to low precision and large fluctuations in temperature control. Based on a new combined positive- and negative-pressure ventilation (CPNPV) mode, a dynamic temperature model is constructed. Additionally, a temperature control method for a layer house is designed using a variable universe fuzzy PID control algorithm (VFPID). First, based on the principles of energy and mass balance, and by decoupling the relationship between positive- and negative-pressure ventilation volumes, a dynamic temperature model for layer houses under CPNPV was established. Then, the PID parameters and the proportional relationship between positive- and negative-pressure ventilation were optimized through fuzzy rules, and a proportional exponential function was introduced to adjust the scaling of the universe, enabling fine-tuned control. Finally, a temperature control model for the layer house was built using Simulink. The results show that the coefficients of determination (R2) of the constructed dynamic temperature models are between 0.79 and 0.88, respectively, indicating high accuracy. The designed VFPID method outperformed traditional on–off control and improved control precision by 20–23.53% and 10.34–22.22% compared with PID control and fuzzy PID(FPID) control methods, respectively. This study provides new insights for the development of environmental control equipment and precise environmental regulation of layer houses.