Micro-tubular protonic ceramic fuel cells (MT-PCFCs) offer significant advantages in energy utilization and storage, including high stability/durability and intermediate working temperature. Inefficient intraluminal current collection and costly fabrication processes are challenges for high-performance MT-PCFCs. Herein, hierarchically structured Ni/Ni–BaCe0.7Zr0.1Y0.2O3-δ dual-layer hollow fibers (DLHFs) have been fabricated by the phase-inversion assisted co-spinning/co-sintering technique. By adjusting the viscosity of anode suspension, the DLHFs' microstructure is tailored and optimized for porosity, pore size, and thickness of collector layer and spongy region. After assembling MT-PCFCs, effects of DLHFs’ microstructure on fuel cell performance are investigated, revealing that a thinner spongy region reduces gas transfer resistance, lowers polarization impedance, and enhances fuel cell performance. A maximum power density of 687.1 mWcm−2 for the optimum MT-PCFC is reached at 700 °C. The innovative DLHF design enhances current collecting efficiency for MT-PCFCs and exhibits potential in other micro-tubular applications, such as hydrogen pumps and electrochemical reactors.