Using cotton stalk lignin as raw material, three kinds of lignin, urea-based modified cotton stalk lignin, esterified lignin and m-phenylenediamine-based modified cotton stalk lignin were prepared and added to polypropylene as polymer modifier. Effects of different modified lignin on the flame retardant and antioxidant properties of polypropylene were studied. The results show that the three kinds of modified lignin improve the flame retardant and antioxidant properties of polypropylene. After adding 15% urea-based modified cotton stalk lignin to polypropylene, the oxidation induction time is increased by 52.9% compared with the pure polypropylene sample; the shear torque is increased by 50.58% at 200 °C, screw speed 30 r/min, and reflux for 10 min. However, after adding 15% m-phenylenediamine-based modified cotton stalk lignin, the oxygen index reaches 24.9%. It can be found in the SEM images that the addition of modified lignin makes polypropylene form a carbon layer during the combustion process, which further demonstrate that the modified lignin enhances the polypropylene flame retardant properties. The mechanical properties results show that with the addition of modified lignin, the mechanical properties of polypropylene are affected to a certain extent.