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Machine learning-based generative models can generate novel molecules with desirable physiochemical and pharmacological properties from scratch. Many excellent generative models have been proposed, but multi-objective optimizations in molecular generative tasks are still quite challenging for most existing models. Here we proposed the multi-constraint molecular generation (MCMG) approach that can satisfy multiple constraints by combining conditional transformer and reinforcement learning algorithms through knowledge distillation. A conditional transformer was used to train a molecular generative model by efficiently learning and incorporating the structure–property relations into a biased generative process. A knowledge distillation model was then employed to reduce the model’s complexity so that it can be efficiently fine-tuned by reinforcement learning and enhance the structural diversity of the …