The circadian clock coordinates the daily rhythmicity of biological processes, and its dysregulation is associated with various human diseases. Despite the direct targeting of rhythmic genes by many best-selling and WHO essential drugs, traditional approaches can’t satisfy the need of explore multi-timepoint drug administration strategies across a wide range of drugs. Here, we developed Chronotoxici-plate, a high-throughput automated rhythmic organoid tool for chronotherapy assessment. We identified Cry1 as a rhythmic marker in DPLOs, providing insights for rapid assessment of organoid rhythmicity. Using Oxaliplatin as a representative drug, we demonstrated time-dependent variations in toxicity on the Chronotoxici-plate, highlighting the importance of considering time-dependent effects. Additionally, we observed improved development of rhythmic organoids, indicating a novel dimension in primary organoid culture. We successfully generated in vitro rhythmic primary organoids within four days, and enabled a preliminary assessment of chronotherapy's drug safety within seven days. This approach holds great promise for reducing drug side effects by optimizing administration timing and expanding the bank of available drugs.