A less-toxic and durable flame-retardant treatment for cotton fabrics was developed using a blocked isocyanate (MDI), citric acid (CA) as a cross-linker, and 3-(dimethylphosphono)-N-methylolpropionamide (MDPPA) as a fire-retardant agent. Treated samples were prepared using the pad–dry–cure method, in which cotton fabric samples were immersed in solutions containing various ratios of MDPPA/CA/MDI. The chemical structures of the treated cotton fabrics, as well as the flame retardancy, thermal stability, physicochemical properties, and durability of the flame-retardant effect to washing, were investigated. The treated cotton fabrics showed different flame retardancies depending on the ratio of components in the flame-retardant treatment, and, thus, the optimal ratio was determined. Using Fourier transform infrared and X-ray photoelectron spectroscopy analyses, we confirmed that MDPPA was attached to the cotton fibers. In addition, vertical flame-retardancy tests were performed on samples before and after washing and the limiting oxygen index values were obtained. Based on the tests, the sample treated with a mixture containing 400, 40, and 50 g/L of MDPPA, CA, and MDI, respectively, showed the best fire resistance, even after 50 washing cycles, and the tear strength, crease recovery angle, and flame retardancy were all improved compared to those of the untreated sample.