As an innovative methodology in data processing and knowledge representation, granular-ball computing (GBC) adaptively generates distinct neighborhoods for individual objects, thereby improving both generality and flexibility. By replacing point inputs with granular-balls (GBs), GBC achieves substantial efficiency gains. However, traditional GB-based classifiers may produce unreliable classifications under uncertain conditions. To address this limitation, we propose a novel approach that integrates three-way decision (3WD) theory with GBC, enabling robust handling of uncertain classification problems. This study first introduces a sequential three-way decision with fuzzy granular-ball rough sets (S3WD-FGBRS). We systematically analyze the changing rules of the multilevel decision cost in S3WD-FGBRS and its three regions. Building upon the principle of justifiable granularity, we develop a cost-sensitive three-way granular-ball generation method (CS3W-GBG) based on S3WD-FGBRS that incorporates a granularity optimization mechanism. To validate our approach, we conduct comprehensive experiments using three state-of-the-art GB classifiers and two benchmark classifiers on 12 publicly available datasets. Experimental results demonstrate that CS3W-GBG exhibits strong resilience in processing uncertain data through its 3WD strategy. Furthermore, our method achieves competitive performance compared to existing approaches in terms of classification accuracy and robustness.