To enhance the output performance of proton exchange membrane fuel cell (PEMFC) under practical stack operating conditions, a novel flow field with variable-density bionic cuttlefish-fin wave-shaped flow field was proposed and a three-dimensional single-phase PEMFC stack model covering inlets and outlets, membrane electrode assembly, and gas flow fields was established. The effects of the density distribution of wave-shaped flow fields on the multi-physics performance of the fuel cell were systematically investigated. By comparing four types of flow fields, namely linear, uniform-wave, dense-to-sparse, and sparse-to-dense flow fields, the influence laws of flow field density on reactant gas distribution, water removal, pressure distribution uniformity, current density, and output power were thoroughly revealed. The results demonstrate that the sparse-to-dense flow field can significantly improve the transport uniformity of reactant gases and enhance water management capability, optimizing the current density distribution and improving the output power. At an operating voltage of 0.6 V, the power density of this flow field structure is 8.5% higher than that of the traditional linear flow field, which fully verifies that the variable-density bionic flow field has important application value and broad application prospects in synergistically optimizing the comprehensive performance of PEMFC stacks.