5-Fluorouracil (5-FU) is one of the important antitumor drugs and is widely used to treat various types of cancers. However, its administration is limited to intravenous route due to poor oral bioavailability. Herein, we hypothesized that the maleimide group-containing 5-FU prodrug (EMC-5-FU) could improve the intestinal mucoadhesion because the maleimide end group can covalently target thiol residues of mucin glycoprotein covering the intestinal enterocytes. In vitro bioadhesion results showed that EMC-5-FU exhibited good affinity to the cysteine-rich subdomains of mucin and NMR studies successfully verified the covalent attachment of EMC-5-FU to mucin. The intestinal perfusion study indicated that the intestinal bioadhesion and membrane permeability are greatly enhanced for EMC-5-FU, in comparison with 5-FU. Mucoadhesion investigations on rat intestine intuitively confirmed increased intestinal retention of 5-FU through maleimide-mediated mucoadhesion. Moreover, AUC of the total 5-FU level for EMC-5-FU solution was 2.65-fold higher compared with 5-FU solution. Our study further suggested that the amphiphilic prodrug EMC-5-FU with good mucoadhesion is a promising delivery strategy form to overcome multiple barriers of oral absorption.