Background: This study aimed to compare three small-area level mortality metrics according to urbanity in Korea: the standardized mortality ratio (SMR), comparative mortality figure (CMF), and life expectancy (LE) by urbanity. Methods: We utilized the National Health Information Database to obtain annual small-area level age-specific numbers of population and deaths in Korea between 2013 and 2017. First, differences in the SMR by urbanity were examined, assuming the same age-specific mortality rates in all small areas. Second, we explored the differences in ranking obtained using the three metrics (SMR, CMF, and LE). Third, the ratio of CMF to SMR by population was analyzed according to urbanity. Results: We found that the age-specific population distributions in urbanized areas were similar, but rural areas had a relatively old population structure. The age-specific mortality ratio also differed by urbanity. Assuming the same rate of age-specific mortality across all small areas, we found that comparable median values in all areas. However, areas with a high SMR showed a strong predominance of metropolitan areas. The ranking by SMR differed markedly from the rankings by CMF and LE, especially in areas of high mortality, while the latter two metrics did not differ notably. The ratio of CMF to SMR showed larger variations in small areas in rural areas, particularly in those with small populations, than in metropolitan and urban areas. Conclusions: In a comparison of multiple SMRs, bias could exist if the study areas have large differences in population structure. The use of CMF or LE should be considered for comparisons if it is possible to acquire agespecific mortality data for each small area.