Due to the physical and chemical effect of polycarboxylate (PCE) ether superplasticizers on the simultaneous hydration of aluminate phase and silicate phase, the structural build-up of cement paste with PCE remains a much-complicated process. In order to reveal the underlying mechanism, this study reports the thixotropic structural build-up of C3S paste with PCE in the early stage (stage I before initial setting, within 1500 s). It should be subdivided into stage I′ (rapid non-linear increase) and stage I″ (slow linear development), since PCE significantly prolongs the duration of stage I′ from ∼10 s to ∼1000 s. Although PCE does not alter the origins of thixotropy (CSH/C3S cohesive forces and colloidal interactions), it can change the magnitude of driving forces, greatly depending on its adsorption in the pseudo-contact region. Consequently, the dominant driving force in stage I′ is C3S cohesive force, while it is colloidal interactions in stage I″. The quantitative models of colloidal percolation characteristic time (tperc) and thixotropic structural build-up rate (Gthix) are developed, both of which are determined by the surface coverage and initial solid volume fraction. Increasing PCE dosage augments tperc and diminishes Gthix, until reaching the maximum adsorption threshold (not full surface coverage), beyond which further PCE increase has a minimal effect on tperc and Gthix.