Kinsey's research was strictly quantitative - he was interested in who had performed what sex acts, with whom, when, under what conditions, etc. His Sexual Behavior in the Human Female (and the companion, Male, work) were based on a series of interviews that were tabulated as data.

Masters and Johnson, in contrast, were interested in the physiology and psychology of sex - so they sought to develop a better understanding of how individual human bodies/minds responded to sex and sexual stimuli.

In short, Kinsey was interested in how frequent or widespread different sexual behaviors were within the population, while Masters and Johnson were interested in understanding how and why humans did those things, and enjoyed those acts (or not).