Soundscape is the production of sounds and the acoustic environment, and it emphasizes peoples’ perceiving and experiencing process in the context. To this end, this paper focuses on the Pearl River Delta in China, and implements an empirical study based on the soundscape evaluation data from the Participatory Soundscape Sensing (PSS) system, and the geospatial data from multiple sources. The optimal variable set with 24 features are successfully used to establish a random forest model to predict the soundscape comfort of a new site (F1 = 0.61). Results show that the acoustic factors are most important to successfully classify soundscape comfort (averaged relative importance of 17.45), subsequently ranking by built environment elements (11.28), temporal factors (9.59), and demographic factors (9.14), while landscape index (8.60) and land cover type (7.71) seem to have unclear importance. Furthermore, the partial dependence analysis provides the answers about the appropriate threshold or category of various variables to quantitatively or qualitatively specify the necessary management and control metrics for maintaining soundscape quality. These findings suggest that mainstreaming the soundscape in the coupled natural–human systems and clarifying the mechanisms between soundscape perception and geospatial factors can be beneficial to create a high-quality soundscape in human habitats.