Herein, we report machine learning algorithms by training data sets from a set of both successful and failed experiments for studying the crystallization propensity of metal-organic nanocapsules (MONCs). Among a variety of studied machine learning algorithms, XGBoost affords the highest prediction accuracy of >90%. The derived chemical feature scores that determine importance of reaction parameters from the XGBoost model assist to identify synthesis parameters for successfully synthesizing new hierarchical structures of MONCs, showing superior performance to a well-trained chemist. This work demonstrates that the machine learning algorithms can assist the chemists to faster search for the optimal reaction parameters from many experimental variables, whose features are usually hidden in the high-dimensional space.