Ionomer impregnation represents a milestone in the evolution of polymer electrolyte fuel cell (PEFC) catalyst layers. Ionomer acts as the binder, facilitates proton transport, and thereby drastically improves catalyst utilization and effectiveness. However, advanced morphological and functional characterizations have revealed that up to 60% of Pt nanoparticles can be trapped in the micropores of carbon support particles. Ionomer clusters and oxygen molecules can hardly enter into micropores, leading to low Pt utilization and effectiveness. Moreover, the ionomer thin-films covering Pt nanoparticles can cause significant mass transport loss especially at high current densities. Ionomer-free ultra-thin catalyst layers (UTCLs) emerge as a promising alternative to reduce Pt loading by improving catalyst utilization and effectiveness, while theoretical issues such as the proton conduction mechanism remain puzzling and practical issues such as the rather narrow operation window remain unsettled. At present, the development of PEFC catalyst layer has come to a crossroads: staying ionomer-impregnated or going ionomer-free. It is always beneficial to look back into the past when coming to a crossroads. This paper addresses the characterization and modeling of both the conventional ionomer-impregnated catalyst layer and the emerging ionomer-free UTCLs, featuring advances in characterizing microscale distributions of Pt particles, ionomer, support particles and unraveling their interactions; advances in fundamental understandings of proton conduction and flooding behaviors in ionomer-free UTCLs; advances in modeling of conventional catalyst layers and especially UTCLs; and discussions on high-impact research topics in characterizing and modeling of catalyst layers.