This prospective study investigated associations of various diet quality indices with mortality in Japan. Participants were 13,355 men and 15,724 women from the Takayama study. Eight diet quality indices were assessed using a food frequency questionnaire: the Dietary Approaches to Stop Hypertension (DASH), Alternative Mediterranean diet scores (AMED), Healthy Eating Index-2015 (HEI-2015), Alternate Healthy Eating Index-2010 (AHEI-2010), Nutrient Rich Food Score 9.3 (NRF9.3), Diet Quality Score for Japanese (DQSJ), Japanese Food Guide Spinning Top (JFGST), and 12-item Japanese Diet Index (JDI12). Cox proportional models estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for all-cause and cause-specific mortality in 1 standard deviation (SD) difference for each index, with adjustment for confounders. During a mean follow-up of 14.1 years, 5,339 deaths were recorded. HRs (95% CIs) per 1 SD higher index were 0.90 (0.87 to 0.93) for AHEI-2010, 0.92 (0.89 to 0.95) for DQSJ, 0.93 (0.91 to 0.96) for NRF9.3, 0.94 (0.92 to 0.97) for AMED and DASH, 0.94 (0.91 to 0.97) for JFGST, 0.94 (0.91 to 0.98) for JDI12, and 0.97 (0.94 to 0.996) for HEI-2015. Similar protective associations were observed for cardiovascular disease mortality, but not for cancer mortality. These findings suggest that all eight indices are associated with lower mortality and that the strength of associations varies across indices; AHEI-2010 showed relatively strong associations, followed by the DQSJ, whereas the associations of HEI-2015 appeared relatively weaker in this Japanese population.