Regulating plant factories is crucial for optimal plant growth and yield. Although LEDs (light-emitting diode) are called cold light sources, more than 80% of the heat is still emitted into the surrounding environment. In high-density vertical agricultural facilities, the crop canopy is positioned close to the light source to maximize light absorption and promote plant growth. LED heat dissipation can cause disturbances in the microclimate of crop canopies, which can lead to tip burn disease in plant crops and result in economic losses for plant factories. CFD (computational fluid dynamics) is used as the main technical tool to simulate and optimize the environment of agricultural facilities. This study utilized Star-ccm+ to simulate the microclimate of plant factories under different light treatments. Uniformity coefficient UI and disturbance coefficient θ were proposed to quantitatively analyze LED heat dissipation’s impact on microclimate. In the T5 treatment group, which had a PPFD of 350 μmol/m2·s in the growth zone and 250 μmol/m2·s in the seedling zone, the relative humidity (RH), airflow, and temperature uniformity coefficients UI were 0.6111, 0.3259, and 0.5354, respectively, with corresponding disturbance coefficients θ of 0.0932, 0.1636, and 0.1533. This study clarifies the degree of perturbation caused by LED heat dissipation on microclimate, providing a theoretical basis for regulating plant factory light and promoting sustainability.