The influences of the anthesis date and the fruiting branch positions on parameters of cotton fiber quality and super-molecular structure were studied. Fiber quality parameters, such as cotton fiber length, micronair, maturity and fiber strength deteriorated with postponing the anthesis date and decreasing temperature. When anthesis happened on the same date, the fruiting branch positions affected the fiber quality parameters, and the fiber quality parameters of the lower portion turned out to be higher than that of the upper portion, although the difference was insignificant. The super-molecular structure of the lower portion turned out to be superior to that of the upper portion at the early anthesis date and high temperature, which is in accordance with what was mentioned above, but the fruiting branch positions did not affect the impact of the anthesis date on the super-molecular structure.