An eco-friendly clay-based synergistic flame-retardant coating was established on cotton fabrics via facile layer-by-layer assembly derived from polyethyleneimine (PEI), attapulgite clay (ATP), and phytic acid (PA). The fabricated flame-retardant (FR) cotton fabrics demonstrated improved thermal stability. Compared to untreated cotton fabrics, the limiting oxygen index of Cotton-8TL was improved to 27.0%. The peak heat release rates of the prepared FR cotton fabrics were lower than that of the pristine cotton fabrics, showing a maximum reduction of 41%. The deposition coating system improved the amount of char residue effectively. The intumescent flame-retardant mechanism was proposed through the analysis of char residue and the suppression properties of volatile gases. Furthermore, compared with those of the untreated cotton fabrics, the tensile strength and elongation at break of the FR cotton fabrics in the warp direction were improved by 20% and 47% remarkably, respectively. A feasible surface modification strategy was provided for the flame-retardant treatment of cotton fabrics with the improvement of mechanical properties.