The invention discloses a system and a method for tumor heterogeneity assessment and particularly provides a molecular clone analysis method. On the basis of various types of variation detection results of high-throughput sequencing in circulating tumor DNA, all variations are divided into different molecular clones to realize tumor heterogeneity assessment by molecular clone levels. By adoption of the method, tumor heterogeneity assessment based on ctDNA high-throughput variation detection is realized to effectively assist in making of tumor prognosis and treatment schemes.