The invention provides a module based thermal insulation cotton filling method. The kiln body of an annealing kiln is mainly composed of an outer frame, an inner frame, an outer side plate, an inner side plate and a thermal insulating layer. The method comprises the following steps: a, separating the outer side plate from the frame of the kiln body; b, fabricating a sidewall thermal insulation cotton mounting hold-down tool; c, horizontally placing a clamping platform on a worktable; d, fabricating a thermal insulation cotton cut template matched with the thermal insulation cotton needing to be packed on the outer side plate in shape and size; e, determining the thermal insulation density of the thermal insulation cotton within the range of 170-180kg/m<3>; f, putting the cut thermal insulation cotton on the outer side plate layer by layer in a sleeving manner; g, compressing the thermal insulation cotton tightly and fixing on the outer side plate to form a sidewall thermal insulation module; h, mounting a compression bar on the screw of the clamping platform, tightening a square nut by use of a hand wheel, pressing the sidewall thermal insulation module in the frame of the kiln body firmly until the outer side plate is held down with the outer frame, and welding the outer side plate on the outer frame; I, finally, demounting the thermal insulation cotton mounting hold-down tool and mounting the inner side plate.