Abstract: Paper-based microfluidic fuel cells, as miniature power sources with significant potential for micro-medical diagnostics and portable electronic devices, offer advantages such as simple structure, low cost, and pollution-free operation. To address the issue of fuel cross-contamination in paper-based batteries, an innovative paper-based flow channel structure incorporating embedded cotton threads is proposed. This design suppresses fuel cross-contamination and enhances the performance of potassium formate paper-based microfluidic fuel cells, thereby promoting the efficient utilization of potassium formate fuel. Analysis of experimental results reveals that homemade paper-based flow channels effectively reduce flow velocity and eliminate solute-solvent stratification compared to commercial filter paper. Increasing the sodium sulfate content in the embedded cotton thread significantly enhances the performance of paper-based batteries. Appropriately increasing fuel concentration effectively reduces activation resistance, thereby enhancing cell performance. Selecting an optimal acid-base environment improves cell performance. At a potassium hydroxide concentration of 1 mol/L, the cell achieves a limiting current density of 10.2 mA/cm² and a peak power density of 2.9 mW/cm², representing the optimal operating conditions in this study.