In order to predict and control the CPAM induced flocculation process for lignin recovery and subsequent dissolved hemicelluloses utilization from pre-hydrolysis liquor (PHL), quantitative population balance model which can describe aggregation, breakage and restructure phenomenon in the flocculation process was developed to describe the process. The simulation results showed, in general, high charge CPAM resulted in lower collision efficiency, lower restructure rate and stronger flocs than the lower charged CPAM. The increase of CPAM dosage had positive effect on collision efficiency and restructure rate and negative effect on energy dissipation rate. With the increase of temperature, low charge density CPAM flocculation system experienced more significant change regarding energy dissipation rate and restructure rate. The collision efficiency was not significantly affected by the temperature change for both CPAMs. Shear rate had negative effect on collision efficiency, positive effect on energy dissipation rate and restructure rate. The addition of salt slightly increased the collision efficiency, decreased the energy dissipation rate for both CPAMs system. More negative effect is observed for high charge density flocculation system.