The objective of this study was to investigate factors affecting whale-watching passengers’ level of comfort and satisfaction by using a questionnaire survey and statistical analysis. This study also examined the correlation between sea state and passenger comfort during the cruise and created a Logistic regression model for estimating passenger comfort. Two types of data were analyzed in this study. One was the in situ observed wave data collected from the whale-watching sea area by a metocean buoy. The other was questionnaire survey data collected from whale-watching passengers. A database was established for the two types of data after they had gone through a data quality control process, and then the data were quantitatively analyzed using Statistical Product and Service Solutions (SPSS) software. The passenger comfort survey results indicated that the motion of ships was the main factor contributing to the passengers’ discomfort, whereas the correlation analysis results revealed that passengers’ seasickness experience and illness ratings (IRs) were highly and significantly correlated with comfort. A literature review also revealed that sea state affects the motion of ships, a key factor contributing to the passengers’ seasickness. The present study demonstrated that comfort and the wave height-to-period ratio were highly correlated. Accordingly, the gender, age, and seasickness experience of whale-watching passengers and the wave height-to-period ratio can be entered into the Logistic regression model established by this study to estimate the passenger comfort on a whale-watching cruise before boarding the ship.