In order to improve the spraying efficiency of cotton chemical topping agents, a field experiment was conducted to compare the effects of 250 g·L−1 mepiquat chloride aqueous solutions sprayed by a T30 unmanned aerial vehicle (UAV) and a boom sprayer. The cotton agronomic parameters, pesticide utilization rate, yield, and fiber quality were determined. The results showed that the pesticide utilization rates of the T30 UAV and the boom sprayer were 48.71% and 30.37%, respectively. After 10, 20, 30, and 40 days of T30 UAV spraying, the plant height inhibition rates of the two varieties of cotton were 12.97%, 13.78%, 20.91%, and 26.14% for Xinluzao 52 and 8.64%, 13.37%, 14.72%, and 18.03% for Huiyuan 720. After spraying with a boom sprayer, the plant height inhibition rates were 7.94%, 11.13%, 18.23%, and 23.69% for Xinluzao 52 and 6.09%, 9.98%, 11.78%, and 15.14% for Huiyuan 720 after 10, 20, 30, and 40 days of spraying. The T30 UAV spraying chemical topping agent was shown to have a significant beneficial effect on the utilization rate of the pesticides, as well as the agronomic properties, yield, and the fiber quality of the cotton.