Myopia is increasing worldwide and its preventable measure should urgently be pursued. N‐3 polyunsaturated fatty acids (PUFAs) have been reported to have various effects such as vasodilative and anti‐inflammatory, which myopia may be involved in. This study is to investigate the inhibitory effect of PUFAs on myopia progression. A lens‐induced myopia (LIM) model was prepared using C57B L6/J 3‐week‐old mice, which were equipped with a −30 diopter lens to the right eye. Chows containing two different ratios of n‐3/n‐6 PUFA were administered to the mice, and myopic shifts were confirmed in choroidal thickness, refraction, and axial length in the n‐3 PUFA‐enriched chow group after 5 weeks. To exclude the possibility that the other ingredients in the chow may have taken the suppressive effect, fat‐1 transgenic mice, which can produce n‐3 PUFAs endogenously, demonstrated significant suppression of myopia. To identify what elements in n‐3 PUFAs took effects on myopia suppression, enucleated eyes were used for targeted lipidomic analysis, and eicosapentaenoic acid (EPA) were characteristically distributed. Administration of EPA to the LIM model confirmed the inhibitory effect on choroidal thinning and myopia progression. Subsequently, to identify the elements and the metabolites of fatty acids effective on myopia suppression, targeted lipidomic analysis was performed and it demonstrated that metabolites of EPA were involved in myopia suppression, whereas prostaglandin E2 and 14,15‐dihydrotestosterone were associated with progression of myopia. In conclusion, EPA and its metabolites are related to myopia suppression and inhibition of choroidal thinning.