Separation of a eutectic-forming mixture is a challenge in the manufacturing process of fine chemical products. In this paper, a novel separation technology for a binary eutectic mixture by solution crystallization combined with particle size fraction was proposed. A eutectic-forming mixture of fluorene and fluorenone was used as the model compounds. On the basis of the determined fluorene-fluorenone-cyclohexane ternary solid-liquid equilibrium phase diagrams, isothermal and polythermal crystallization experiments of a fluorene-fluorenone eutectic mixture with different concentrations were performed in cyclohexane. Results showed that two product-rich parts (fluorene-rich part and fluorenone-rich part) and a mixture part were obtained at the same time under isothermal and polythermal mode by sieve fraction. Furthermore, changing the initial composition slightly from the eutectic point could improve the polythermal crystallization process significantly and achieve a higher yield. In addition, an enhanced online removal separation process was employed after crystallization, and it attained two products of fluorene and fluorenone with a purity of 90.17 and 95.30 wt %, respectively. To date, this has been the first experiment that attempted to separate a eutectic system from the view of particles size and purity.