Cationic polymer can effectively improve the clay tolerance of polycarboxylate superplasticizer in cement pastes, but the thixotropy of fresh cement pastes in presence of cationic polymer has not received sufficient attention. In this paper, the effect of cationic polymer on the thixotropy of fresh cement pastes containing Na-bentonite was studied. The hydration heat was considered and measured. Besides hysteresis loop areas, the destruction and reconstruction of flocs in thixotropic behaviors of cement pastes were also investigated. The results showed that the cationic polymer delayed the release of cement hydration and decreased the total hydration heat. Cement hydration improved the thixotropy of cement pastes. An obvious decrease of hysteresis loop areas of cement pastes was observed with the addition of cationic polymer, which indicated the decrease of the thixotropy. The equilibrium shear stress, characteristic time of destruction of flocs and incipient structural parameter in thixotropic behaviors were also decreased with the addition of cationic polymer. On the other hand, cationic polymer increased the reconstruction rate of flocculated structure in cement pastes.