The dispersion of cellulose nanocrystals (CNCs) in suspensions determines the quality of the CNC-reinforced composites. Before being mixed into the composite matrix, stable suspensions must maintain a well-dispersed state, requiring proper design strategies to prevent agglomeration and precipitation. Considering the volume fraction, aspect ratio, and zeta potential, this paper proposes a coarse-grained model to simulate CNC clustering and an experimental program to observe accelerated precipitation of CNCs. High-throughput molecular dynamics simulations yield a diagram of clustering time plotted against aspect ratio, zeta potential, and volume fraction of CNCs. Turbidity analysis with centrifugation-accelerated tests shows that precipitation occurs only after clustering and agglomeration are completed and that centrifugation rarely accelerates clustering. Clustering of short chains instantly leads to agglomeration, whereas clustering of long chains features delayed agglomeration, which can be triggered by centrifugation. Zeta potential is found to be the most critical factor affecting clustering, agglomeration, and precipitation. The findings provide critical insights into the conditions that favor stable CNC suspensions, which are essential for preparing well-dispersed suspensions and improving the composite material performance.