The influences of boron on the content of pectin and boron fraction in two cotton cultivars with different boron efficiency were studied under the condition of solution culture experiments. The content of pectin and different boron fraction in the boron-inefficient cotton cultivar was much greater than those in boron-efficient one at sufficient boron supply. However, the content of water soluble pectin and protopectin in boron-efficient cultivar was more than those in boron-inefficient one under boron deficiency. Severe boron deficiency significantly depressed the content of water soluble boron and acid soluble boron in both cotton cultivars, especially water soluble boron. Moreover, the reduce degree of acid soluble boron in all parts and water soluble in the young leaves of the inefficient cultivar was greater than those of the efficient one, but that of water soluble boron in the old leaves and roots was less than that of the efficient one. Boron deficiency increased the ratio of water soluble boron content in young leaves to old leaves of both cultivars, especially the boron-efficient one. The difference of the ratio was greater than that of the content of water soluble boron or acid soluble boron between both cotton cultivars with different boron efficiency, it might be a better index to reflect the difference of boron efficiency among genotypes.