To study the effects of the interface thermal resistance on surface morphology evolution in precision glass molding (PGM) for microlens array with different mold materials, including Tungsten carbide and heat-resistant stainless steel, the glass-mold interface thermal resistance is calculated, and heat-transfer simulation of PGM based on an interface thermal resistance model at the heating stage is conducted correspondingly. The effect of flattening behavior on the glass-mold interface is explained. Then, experiments evaluating the relationship between heating time and glass surface roughness are carried out, and the glass adhesion phenomenon appearing on the heat-resistant stainless steel mold is observed and analyzed. Finally, the microlens array is fabricated on the nickel phosphorous plating layer on the heat-resistant stainless steel substrate by diamond-ball nose-end milling, and experiments of PGM for the microlens array are carried out to verify the interface thermal resistance model. The result shows that a high-quality surface can be obtained by the combination of a smooth mold and rough glass. Compared with the microlens array fabricated with the rough glass preform, using the smooth glass preform achieves higher form accuracy without defects or blurs.