A new rheological methodology is used to quantify the kinetics and thermal activation of thixotropic recovery (flocculation) of uncrosslinked carbon black–reinforced emulsion SBR following high shears and over a range of annealing temperatures. A wide range of carbon black types are examined to determine the influence of aggregate morphology and surface area on compound flocculation. Several kinetic parameters are correlated with the carbon black aggregate structure and surface area, the results of which imply a transition in mechanisms controlling modulus recovery between shorter and longer recovery time scales. Thermal activation of flocculation is found to scale to the surface area and to the mean aggregate diameter of the carbon blacks following power law relationships. The thermal activation data for a subset of compounds with different carbon blacks prepared at different loadings collapses onto a single master line by rescaling the data to a parameter that is proportional to the theoretical interparticle force calculated for the idealized situation of two spherical particles in proximity. Three different van der Waals force models are evaluated, and in each case, an effective superposition of the thermal activation data is achieved. This indicates that the attractive force between aggregates plays a key role in the flocculation of carbon black in rubber, and this force can be traced back to the aggregate and primary particle sizes, interaggregate distances, and effective volume fractions. The activation energy for the viscosity of the unfilled, uncrosslinked SBR is similar to analogous values calculated for the thermal activation of flocculation. This coupling of energetics may be the result of creep/flow of rubber out of gaps between aggregates resulting from interaggregate attractive forces and any potential diffusive motion of the aggregates. Bound rubber data appear to contain information relating to aggregate packing, which could be exploited in future work to further explore the mechanism of flocculation.