"Autistic traits" include a wide range of severity levels. They are often subclinical, and widely distributed in the general population. It is possible that food selectivity due to hyper- or hypo-reactivity to smell or texture, an autistic feature, may result in inadequate nutrient intakes even among non-clinical adults with autistic traits. However, dietary intake of adults with autistic traits has not been elucidated. This study aimed to investigate an association between dietary intake and autistic traits. We cross-sectionally analyzed data of 1440 men and 613 women extracted from the Eating Habit and Well-Being study. Autistic traits were assessed using the Japanese version of the Subthreshold Autism Trait Questionnaire (SATQ), and dietary intake was assessed using a validated food frequency questionnaire. Iron and vitamin B intakes were marginally and inversely associated with the SATQ score in men. The SATQ score in women was positively associated with carbohydrate intake, but had an inverse association with protein, mineral, vitamin, and dietary fiber intakes. Low intakes of seaweed, fish and shellfish, and vegetables were observed in participants with severe autistic traits. Associations of autistic traits with food selectivity and low nutrient intakes should be further investigated to promote a new dietary strategy in the general population.