The present disclosure provides a method for training a molecular binding model, and a molecular screening method and apparatus, which can be applied in the field of intelligent medicine, and used to solve the problem of low molecular screening accuracy. The screening method comprises: using a molecular binding model to be trained, determining binding activity feature information, embedded feature information and eutectic feature information between a sample protein molecule and a sample candidate molecule, on the basis of protein feature information and molecular feature information; on the basis of the binding activity feature information, the embedded feature information and the eutectic feature information, determining a training loss of the molecule binding model to be trained; if the training loss meets a training target, outputting the molecular binding model as a trained molecular binding model, the trained molecular binding model being used to determine binding activity feature information between a target protein molecule and a target candidate molecule, so as to predict binding activity of a compound after the target protein molecule and the target candidate molecule are virtually bound.