Crohn's disease (CD) is a chronic condition that affects the gut and has adverse effects on growth and development. There is a global increase in the incidence and prevalence rates, and several factors are believed to contribute to this rise, including dietary habits. In contrast, the use of enteral nutrition (EN) as an exclusive source of nutrition is increasingly becoming the preferred induction treatment of pediatric CD patients in part to address the nutrition complications. However, EN therapy is considered less effective in adults with CD. A better understanding of the molecular mechanisms of enteral therapy will help improve the clinical management of CD. It is increasingly becoming evident that the therapeutic utility of EN is in part due to the reversal of the microbial changes and the direct immunomodulatory effects. Moreover, there is a potential tendency for enhancing the efficacy of EN therapy by improving the palatability of the given formulas and, more important, by magnifying the anti-inflammatory properties. Recent observations have shown that the immunomodulatory effects of EN are mediated at least in part by blocking nuclear factor-κB. Furthermore, it is likely that several ingredients of EN contribute to this activity, in particular glutamine and arginine amino acids. In addition, manipulating the composition of EN therapy by altering concentrations of the key ingredients is found to have the potential for more efficient therapy. In this review, the underlying mechanisms of EN actions will be discussed further with a focus on the potential methods for enhancing the efficacy.