It is important to accurately estimate the capacity of the battery in order to extend the service life of the battery and ensure the reliable operation of the battery energy storage system. As entropy can quantify the regularity of a dataset, it can serve as a feature to estimate the capacity of batteries. In order to analyze the effect of voltage dataset selection on the accuracy of entropy-based estimation methods, six voltage datasets were collected, considering the current direction (i.e., charging or discharging) and the state of charge level. Furthermore, three kinds of entropies (approximate entropy, sample entropy, and multiscale entropy) were introduced, and the relationship between the entropies and the battery capacity was established by using first-order polynomial fitting. Finally, the interaction between the test conditions, entropy features, and estimation accuracy was analyzed. Moreover, the results can be used to select the correct voltage dataset and improve the estimation accuracy.