Developing a gel polymer electrolyte with a cross-linked structure is one of the best choices to improve the mechanical strength of the gel polymer electrolyte without sacrificing its lithium-ion transportation properties. However, the cost is always too high. Herein, a novel gel polymer electrolyte based on three-dimensional cross-linked chitosan-poly(ethylene glycol) diglycidyl ether macromolecule network was designed and synthesized through a simple and environmental harmless method, with sustainable and cheap chitosan as major material. The obtained gel polymer electrolyte shows improved mechanical strength of 5.5 MPa, which is higher than that of other gel polymer electrolytes without inert frameworks. The optimized gel polymer electrolyte exhibits a good lithium ionic conductivity of 2.74 × 10 S cm with a superior lithium-ion transfer number of 0.869 at 25 °C. Lithium battery assembled with this gel polymer electrolyte demonstrates an initial discharge capacity of 146.8 mA h g, which retains 88.49% capacity after 360 cycles at 0.2C. Moreover, this gel polymer electrolyte possesses good interfacial compatibility with lithium anode. Therefore, the growth of lithium dendrite is greatly delayed. This research proves the great possibility of applying sustainable and cost-effective chitosan into gel polymer electrolyte and lithium batteries.