An encoding method, a decoding method, and a storage medium are provided. The encoding method includes: determining that a current block is allowed for applying a neural network-based in-loop filtering technique; acquiring a first reconstructed image of the current block; acquiring a first edge image of the current block; inputting the first reconstructed image and the first edge image into a neural network-based in-loop filtering model to obtain a filtered image of the current block; performing cost calculation based on an original image and the filtered image of the current block to determine a first cost value; determining whether the neural network-based in-loop filtering technique is applied to the current block based on the first cost value, and setting first indication information of the current block; and encoding the first indication information, and writing obtained encoded bits into a bitstream.