As a very promising biofuel or fuel additive, the synthesis of 5-ethoxymethylfurfural (EMF) directly from renewable carbohydrates is an important biomass transformation process. Herein, a novel bifunctional catalyst has been successfully synthesized via a Pickering high internal phase emulsion (HIPE) template and pore-filled strategy and employed for the production of EMF from glucose in a one-pot manner. Catalytic results indicated that the grafted Cr3+ by the atom transfer radical polymerization (ATRP) method smoothly processed the isomerization of glucose to intermediate fructose and that the accessible -SO3H and Cr3+ active sites coexisted in the obtained bifunctional catalyst possessing synergistic effects. A high EMF yield of 48.1% was achieved under optimal reaction conditions in an ethanol/tetrahydrofuran (THF) medium. Besides, employing inulin, sucrose, cellobiose, maltose, and starch as the starting materials excellent EMF yields were also obtained over the developed bifunctional catalyst. This study offers new insights into the design of functional catalysts anchoring desirable active sites, and also highlights their applications for biomass transformation.