This work investigates the effect of the addition of NaOH on the compatibility and material properties of thermoplastic starch-zein composite films produced by a twin-screw extruder. Thermoplastic starch-zein composite films were produced by melt extrusion of glycerol-plasticized starch and zein (3:1 ratio) treated with different concentrations of sodium hydroxide (NaOH) (0 M, 0.05 M, 0.1 M, and 0.2 M NaOH). Scanning Electron Microscope and Confocal laser Scanning Microscope revealed that the composite without NaOH formed a phase-separated morphology with large zein aggregates within the starch matrix. However, the increase in NaOH concentration reduced the size of zein aggregates within the starch-zein composite films, with 0.2 M NaOH having the smallest size of zein aggregates. Dynamic mechanical analysis showed a decrease in glass transition temperature (Tg) and storage modulus (E'), suggesting more molecular chain mobility and efficient plasticization of starch and zein. This efficient plasticization was also confirmed by Fourier-Transform Infrared spectroscopy (FTIR). As a result, there was an optimal increase of 28% in elongation at break in the starch-zein composite film with 0.2 M NaOH. In conclusion, compatible thermoplastic starch-zein composite films with improved elongation at break can be produced with a twin-screw extruder by adding 0.2 M NaOH.