PtO2 nanocatalysts-loaded SnO2 multichannel nanofibers (PtO2-SnO2 MCNFs) were synthesized by single-spinneret electrospinning combined with apoferritin and two immiscible polymers, i.e., poly(vinylpyrrolidone) and polyacrylonitrile. The apoferritin, which can encapsulate nanoparticles within a small inner cavity (8 nm), was used as a catalyst loading template for an effective functionalization of the PtO2 catalysts. Taking advantage of the multichannel structure with a high porosity, effective activation of catalysts on both interior and exterior site of MCNFs was realized. As a result, under high humidity condition (95% RH), PtO2-SnO2 MCNFs exhibited a remarkably high acetone response (R-air/R-gas = 194.15) toward 5 ppm acetone gases, superior selectivity to acetone molecules among various interfering gas species, and excellent stability during 30 cycles of response and recovery toward 1 ppm acetone gases. In this work, we first demonstrate the high suitability of multichannel semiconducting metal oxides structure functionalized by apoferritin-encapsulated catalytic nanoparticles as highly sensitive and selective gas-sensing layer.