Missense mutations could affect the Liquid-Liquid Phase Separation (LLPS) propensity of proteins and lead to aberrant phase-separating behaviours, which are recently found to be associated with many diseases including Alzheimer's and cancer. However, the regulatory role of mutations in LLPS remains unclear due to challenges in accurately characterizing the LLPS ability of mutants, including the high similarity in features, lack of labeled data, and vast amounts of data involved. To bridge this gap and facilitate the discovery of therapeutic strategies, we propose the first machine learning-based guider for protein phase-separating behaviour alteration, PScalpel. PScalpel leverages both structural information and an auxiliary tasks-based graph contrastive learning framework to distinguish the mutants’ LLPS ability, and incorporates a genetic algorithms-based recommendation method to identify mutants with desired LLPS properties. Comprehensive computational and biological experiments validate the effectiveness of PScalpel as a versatile tool for guiding alterations in protein phase separation behavior.