Objectives Hataedock is an orally-administered herbal extract that used to treat toxic heat and help excrete meconium accumulates in the fetus from pregnancy. This study compared the effects of Hataedock using the extract of Douchi and omega-3 to control inflammation in the colonic mucosa. Methods NC/Nga mice were divided into three groups; Control group (no treatment), FGT group (given the extract of Douchi), and O3T group (given omega-3). The 3-week-old mouse from each group were given the extract of Douchi and omega-3. After 2 weeks, the colonic mucosa tissues of the mice were observed via Immunohistochemical staining for IL-4, IL-13, CD40, $Fc{\varepsilon}RI$, $p-I{\kappa}B$, EGF in the intestinal mucosa. Results In both FGT and O3T group, IL-4, IL-13, STAT-6 levels and CD40-positive reactions were decreased. However, EGF-positive responses were increased. FGT group showed 35% decrease in IL-4, 45% decrease in IL-13, 48% decrease in CD40, 50% decrease in $Fc{\varepsilon}RI$, 54% decrease in $p-I{\kappa}B$, 52% increase in EGF compared to the control group. O3T group also showed 14% decrease in IL-4, 23% decrease in IL-13, 22% decrease in CD40, 29% decrease in $Fc{\varepsilon}RI$, 41% decrease in $p-I{\kappa}B$, 39% increase in EGF compared to the control group. Conclusions Both early administration of Douchi extract and omega-3 were effective in regulating Th2, relieving inflammation and developing colonic mucosal tissues. Hataedock with Douchi extract may be more effective in modulating immune system in colonic mucosa than omega-3.