In the 21st century, the strategic importance of islands is greatly highlighted. The quality of human settlements is one of the necessary indicators of island cities. However, until recently there have been few reports on quality evaluations of human settlements in island cities. Therefore, based on the theory of human settlements, a comprehensive quality evaluation system on the human settlements of island cities was conducted in the present study. Two typical island cities of the Xiamen and Pingtan Comprehensive Experimental Zone were chosen and their human settlement qualities during different periods were carefully explored and compared respectively. The results show that:(1) the human settlement quality of the two island cities is relatively stable, whereas the livability of Xiamen was higher than that of Pingtan and the gap between them gradually increased; (2) the urban human settlements were correlated with urban economic systems and the degree of correlation between them varied in different stages; (3) the human settlements of the two island cities was comprehensively affected by the subsystems, such as natural, human, social, residential, and support systems, respectively, and the roles of each subsystem were obviously different. The human settlements of Pingtan, which is at the early stage, presented some significant characteristics:the natural system aligned to some extent with the human system and changed to a small degree, whereas the contribution of the social, residential and support systems steadily increased. The human settlements of Xiamen, which is in a more developed stage, presented different characteristics; the natural system was relatively stable, whereas the variations in the human system increased slightly, and the contribution of the social, residential, and support systems were relatively high. The present study provides valuable references for the sustainable development of human settlements of Xiamen and Pingtan Comprehensive Experimental Zone and other similar island cities. Simultaneously, it enriches the empirical cases and human settlement theory.