Methods of encoding and decoding a speech signal using a neural network model that recognizes sound sources, and encoding and decoding apparatuses for performing the methods are provided. A method of encoding a speech signal includes identifying an input signal for a plurality of sound sources; generating a latent signal by encoding the input signal; obtaining a plurality of sound source signals by separating the latent signal for each of the plurality of sound sources; determining a number of bits used for quantization of each of the plurality of sound source signals according to a type of each of the plurality of sound sources; quantizing each of the plurality of sound source signals based on the determined number of bits; and generating a bitstream by combining the plurality of quantized sound source signals.