Hydrophilic fabric materials can absorb electrolyte by capillary action, and higher mechanical strength and device stretchability can be obtained when they are used as substrates of microfluidic fuel cell (MFC). This study aims to explore the effects of four natural polysaccharides on the performance of cotton thread-based flow channel of MFC. Sodium formate and hydrogen peroxide were fuel and oxidant of MFC respectively, combined with graphite tube anode and graphite rod cathode, and polysaccharide modified cotton thread was the flow channel material. Different concentrations of chitosan, guar gum (GG), flaxseed gum (FG), and Sa-son seed gum (SSG) were doped to modify cotton threads and improve the MFC performance. SEM-EDS, XRD, contact angle, FTIR and thermal analyses suggested that the intermolecular interaction between added polysaccharide and cotton cellulose achieved the improved hydrophilicity of the modified threads, consistent with quantum chemical calculations. The optimal Pt/C loading on the anode was 2.5 mg/cm2; the thread size, fuel/anolyte concentration and their interactions markedly influenced the electricity production of MFC. With doped chitosan of 0.5 g/L, the power density (PD) of MFC reached 12.58 mW/cm2, 2.1 times that of MFC with unmodified thread. PD achieved by adding GG, FG and SSG was 11.34, 10.68 and 8.06 mW/cm2, respectively. The differential charge, functional groups, and monosaccharide composition of four polysaccharides may explain their different effects on electrogenesis, which was further supported by EIS and path modeling. The proposed polysaccharide modifications of MFC channel inspire further endeavor in improving micro power sources for niche devices.