The structure of the catalyst layer of PEFCs has a considerable influence on the cell performance. The catalyst layer is manufactured by coating a suspension consisting of Pt/C catalyst particles and a Nafion solution. In a catalyst layer, the decrease in the Pt/C particle agglomeration controlled by the coating condition was reported to improve the performance; however, the influence that the coating condition exerts on the structure and then performance of the catalyst layer when the compositions of suspension are different has not yet been researched well. In this study, we researched a method to control the structure of a catalyst layer by the coating condition and suspension composition. The surface structure, which is well correlated with the predicted number of agglomerated Pt/C particles, showed good agreement with the performance. Under the condition where the Pt/C particles are not dispersed well, the performance was improved with an increase in the coating speed and Nafion content. However, that improvement became negligible at the optimum Nafion content providing maximal cell performance. Further, at a higher Nafion content, the excessive dispersion of Pt/C particles in the catalyst layer deteriorated the performance drastically. These results imply that the performance improvement by coating is effective when the suspension shows fairly high viscosity. Further, a little addition of solvent to decrease the viscosity also improves the performance; however it may be deteriorated by an excessive addition.