The invention relates to a method for preparing a polyamide double-layer microcapsule. The method comprises the following steps: firstly, preparing a polyamide single-layer microcapsule through a micro-channel; utilizing the higher specific surface area and permeability of a microcapsule film to introduce water into the microcapsule; forming an oil-in-water structure in the microcapsule; and adding a certain amount of amine into water and triggering the polymerization reaction on an oil water interface in the microcapsule, thereby acquiring the polyamide double-layer microcapsule. The scale of the microcapsule can be adjusted by adjusting the flow rate of continuous phase and dispersion phase. The morphological feature of the microcapsule is utilized to prepare a multi-chamber microcapsule; the method for coupling with the micro-channel is more convenient in operation and lower in production cost; the method is suitable for different polymer microcapsules having interfacial polymerization reaction; and the slow release performances of the prepared double-layer microcapsule and the single-layer microcapsule are in huge difference.