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The viscosity is a foundational parameter of biomacromolecule in the food industry. The viscosity of macroscopic colloids is closely related to the dynamical behaviors of mesoscopic biomacromolecule clusters, which are difficult to be investigated at molecular resolution by common methods. In this study, based on experimental data, multi-scale simulations combining microscopic molecular dynamics simulation, mesoscopic Brownian dynamics simulation, and macroscopic flow field construction were used to investigate the dynamical behaviors of mesoscopic clusters of konjac glucomannan (KGM) colloids (~500 nm) over a long time (~100 ms). Numerical statistical parameters of the mesoscopic simulation of macroscopic clusters were proposed and proved to represent the viscosity of colloids. Based on the intermolecular interaction and macromolecular conformation, the mechanism of the shear thinning effect was revealed as both the regular arrangement of macromolecules at low shear rates (<100 s−1) and structural collapse of macromolecules at high shear rates (>500 s−1). Then, the effect of molecular concentration, molecular weight, and temperature on the colloid viscosity and cluster structure of KGM colloids was investigated by experiments and simulations. This study provides a novel multi-scale numerical method and insight into the viscosity mechanism of biomacromolecule. The viscosity mechanism of konjac glucomannan colloids was investigated by experiments and multi-scale simulations. [Display omitted] [ABSTRACT FROM AUTHOR]