Polymer electrolyte membrane fuel cell (PEMFC) technology has required significant cost competitiveness for mass commercialization of fuel cell electric vehicle. In order to lower the price of the fuel cell, studies are being conducted to achieve high performance while maintaining the same amount of platinum loading in catalyst layer (CL). In this study, the performance improvement was observed by using Nafion fiber which has proton conductivity as a 1-dimensional material. Two different structures of the catalyst layer according to the diameter control of Nafion fiber are presented. Depending on the difference of size between Nafion fiber diameter and the catalyst layer thickness, a catalyst layer with a macroscopic proton channel (Nafion fiber embedded-CL) and a catalyst layer with an extended gas-catalyst layer interface (Nafion fiber supported-CL) were implemented. Nafion fiber embedded CL showed 33% improved cell performance at 0.6V due to the increase of the proton transport. Nafion fiber supported CL showed 25% improved cell performance at 0.4V due to the increase of the gas transport. From the results of each of the proton and gas transport enhancement, Nafion fiber matrix can be applied as a flexible versatile platform for catalyst layer structure modulation to improve fuel cell performance.