To date, a limited number of studies have examined aspects of food choice values and food literacy in relation to some aspects of dietary behaviors. The aim of this cross-sectional study was to comprehensively examine the associations of food choice values and food literacy with diet quality. In total, 2231 Japanese adults aged 19–80 years completed questionnaires asking about food choice values (accessibility, convenience, health/weight control, tradition, sensory appeal, organic, comfort, and safety) and food literacy characterized by nutrition knowledge, cooking skills, food skills, and eating behaviors (hunger, food responsiveness, emotional overeating, enjoyment of food, satiety responsiveness, emotional undereating, food fussiness, and slowness in eating). As a measure of diet quality, the Healthy Eating Index-2015 (HEI-2015) was calculated using a brief-type diet history questionnaire (BDHQ) or a food combination questionnaire (FCQ). In males, after adjustment for potential confounding factors (including age, body mass index, and the ratio of reported energy intake to estimated energy requirement), the HEI-2015 derived from BDHQ and that derived from FCQ were associated significantly (P ≤0.02) and positively with the food choice value of organic and inversely with food fussiness. In females, the HEI-2015 showed positive associations with the food choice value of health/weight control, nutrition knowledge, and cooking skills and an inverse association with food fussiness, irrespective of the dietary assessment questionnaire (P ≤0.03). In conclusion, this study suggests that several aspects of food choice values and food literacy were associated with diet quality, and the aspects related differed between males and females.