The Cauchy-Schwarz (CS) divergence was developed by Príncipe et al. in 2000. In this paper, we extend the classic CS divergence to quantify the closeness between two conditional distributions and show that the developed conditional CS divergence can be simply estimated by a kernel density estimator from given samples. We illustrate the advantages (e.g., rigorous faithfulness guarantee, lower computational complexity, higher statistical power, and much more flexibility in a wide range of applications) of our conditional CS divergence over previous proposals, such as the conditional KL divergence and the conditional maximum mean discrepancy. We also demonstrate the compelling performance of conditional CS divergence in two machine learning tasks related to time series data and sequential inference, namely time series clustering and uncertainty-guided exploration for sequential decision making. The code of conditional CS divergence is available at https://github.com/SJYuCNEL/conditional_CS_divergence.