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Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs) are driven by recurrent driver mutations and evolve through the stepwise accumulation of additional genetic alterations and clonal evolution. Some large cohort studies have demonstrated that individual additional mutations significantly influence prognosis, leukemic transformation, and progression to myelofibrosis. Furthermore, certain mutations frequently co-occur with other adverse mutations and may act as molecular hubs that amplify clinical impact. Based on these findings, mutation-integrated scoring systems have been developed to improve risk stratification and refine therapeutic decision-making. However, despite the recent adoption of comprehensive genomic testing in clinical practice, there is still limited evidence to guide treatment selection or determine the optimal timing of therapeutic intervention based on mutational profiles or molecular monitoring results. A deeper understanding of clonal evolution, grounded in genomic abnormality data, will be essential for establishing more rational and biology-driven therapeutic strategies.