Optimizing　the　flow　channel　structures　can　improve　the　efficiency　of　proton　exchange　membrane　fuel　cells　and　promote　the　efficient　utilization　of　clean　energy.　This　study　investigates　the　impacts　of　rectangular-baffle　and　tapered　flow　channels　on　electrical　performance,　temperature　distribution　and　mass　transfer　of　proton　exchange　membrane　fuel　cells,　based　on　a　3D,　multi-physical　model.　The　equivalent　average　depth　is　adopted　as　the　reference　benchmark　to　mitigate　the　influence　of　channel　depth.　Results　indicate　that　adopting　variable-depth　channels　enhances　convective　mass　transfer　on　the　porous　layer　surface　under　higher　voltage.　The　convective　mass　transfer　of　oxygen　is　dominant　in　the　activation　polarization　region,　while　diffusion　is　dominant　in　the　concentration　polarization　region.　Variable-depth　channels　enhance　heat　and　mass　transfer　in　comparison　to　the　straight　channel.　The　tapered　channel　can　improve　the　mass　transfer　flux　in　oxygen　starvation　region,　and　the　drainage　ability　of　the　rectangular　baffle　channel　is　inferior　to　the　tapered　channel.　The　rectangular　baffle　channel　demonstrates　better　convective　heat　transfer　performance　and　temperature　uniformity.　A　rectangular-baffle　channel　can　increase　net　power　by　4.31%,　while　a　tapered　channel　can　achieve　a　maximum　increase　of　9.27%　when　the　pumping　power　is　considered.　Therefore,　incorporating　a　tapered　channel　is　an　optimal　strategy　to　boost　cell　efficiency.