Cotton is one of the most important natural fibers and plays a significant role in the national economy of Myanmar. Cotton production in Myanmar is quite low, and the major factor for low cotton production is largely due to sucking pest damage. The cotton aphid Aphis gossypii is a particularly harmful pest; it causes a number of problems such as yield loss and reduction of fiber quality. However, there are limitations of relying on chemical pesticides alone. In the present study, we examined the effectiveness of IPM combining transgenic cotton, intercropping with green gram and botanical neem pesticides on cotton aphid control. In three consecutive planting seasons, the density of cotton aphids was significantly much lower in IPM cotton fields than BT cotton fields with chemical pesticide application. Moreover, the cotton aphid density with IPM practice was kept below the action threshold level for pesticide application (< 10 aphids per leaf or 10% damaged or infested plants) throughout the experimental seasons. The densities of natural enemies of cotton aphids, i.e., coccinellid beetles, lacewings and spiders, were significantly much higher in IPM fields, suggesting that the low aphid density was at least partly thanks to natural enemies. The use of botanical neem pesticides, particularly early in the cotton season, appeared to reduce cotton pests without the use of chemical insecticides and help conserve numerous natural enemies. Cotton yields were not different between IPM and conventional fields. Thus, combination of the IPM components applied here was effective enough to manage cotton aphids, conserve natural enemies, and reduce chemical pesticide use, while keeping cotton production.