Cracking knuckles can make them bigger in that they become swollen. In one study, knuckle cracking caused a "higher incidence of hand swelling and lower grip strength in people who admitted to being habitual knuckle crackers," according to Dr. Henry Bernstein. However, there is no decisive evidence that knuckle cracking causes knuckles to consistently become bigger or more susceptible to arthritis.
Knuckles crack because bubbles form in the joint fluid. When pressure is applied to the joint, the gas bubble pops, which produces the "cracking" sound. In order to truly damage the knuckle, excessive force would be necessary. The forces of knuckle cracking are insufficient to do so.