Cruise ships are distinguished as special passenger ships, transporting passengers to various ports and giving importance to comfort. High comfort can attract lots of passengers and generate substantial profits. Vibration and noise are the most important indicators for assessing the comfort of cruise ships. Existing methods for analyzing vibration and noise data have shown limitations in uncovering essential information and discerning critical disparities in vibration and noise levels across different ship districts. Conversely, the rapid development in machine learning present an opportunity to leverage sophisticated algorithms for a more insightful examination of vibration and noise aboard cruise ships. This study designed a machine learning-driven approach to analyze the vibration and noise data. Drawing data from China’s first large-scale cruise ship, encompassing 127 noise samples, this study sets up a classification task, where decks were assigned as labels and frequencies served as features. Essential information was extracted by investigating this problem. Several machine learning algorithms, including feature ranking, selection, and classification algorithms, were adopted in this method. One or two essential noise frequencies related to each of the decks, except the 10th deck, were obtained, which were partly validated by the traditional statistical methods. Such findings were helpful in reducing and controlling the vibration and noise in cruise ships. Furthermore, the study develops a classifier to distinguish noise samples, which utilizes random forest as the classification algorithm with eight optimal frequency features identified by LightGBM. This classifier yielded a Matthews correlation coefficient of 0.3415. This study gives a new direction for investigating vibration and noise in ships.