A novel healthy diet index for dietary quality can be used to assess food intake. After the Great East Japan Earthquake in 2011, the Fukushima Health Management Survey collected dietary data using a short-form food frequency questionnaire (FFQ). The current study included eligible participants (n = 64,909) aged 16–84 years who answered the FFQ in 2011. The year- and sex-specific dietary patterns were determined via principal component analysis. Based on the typical Japanese, juice/dairy, and meat patterns, healthy diet index (HDI) scores were assigned for food items, resulting in Spearman’s correlation coefficients of 0.730, −0.227, and −0.257, respectively. The mean (standard deviation) of the HDI scores (range: 1–18) were 9.89 (2.68) in men and 9.96 (2.58) in women. Older individuals, women, nonsmokers, those in good health and with regular physical exercise, and those who did not transfer residences had a high HDI score. In the confirmatory analysis, the adjusted odds ratio (95% confidence interval) of the highest vs. the lowest quartiles of HDI scores was 0.87 (0.80, 0.94) for overweight, 0.89 (0.81, 0.97) for large waist circumference, and 0.73 (0.66, 0.80) for dyslipidemia. The HDI score obtained using the FFQ can be applied to evaluate dietary profiles.