Quercus mongolica Fisch. ex Ledeb. and Q. variabilis Blume are two main oak species in China, producing large amounts of acorns every year. However, the trait variations in acorns, as a promising energy crop material, are not fully understood, hence we compared the traits of acorns from the different populations with the altered geographic distribution in this study. Thirteen acorn traits, including phenotype, proximate compositions and functional compounds, were analyzed in both Quercus L. species collected from 44 populations across China. The results showed that, except large differences found among accessions in acorn sizes, the starch varied from 140.96–297.09 mg/g in Q. mongolica and 130.99–306.28 mg/g in Q. variabilis, indicating its substantial differences among populations. The total polyphenols, total flavonoids and soluble tannins varied from 41.76–158.92, 23.43–91.94, and 15.11–17.81 mg/g, respectively, in Q. mongolica, 89.36–188.37, 50.59–116.07, 15.24–17.33 mg/g, respectively, in Q. variabilis, demonstrating their large variations in the levels of polyphenols among populations. Moreover, the acorns of Q. mongolica in North China and Q. variabilis in Southwest China had higher levels of starch and polyphenols. As the geographical location approached in the distribution of two Quercus species, the difference in acorn sizes gradually increased, while that in polyphenols were opposite. Principal component analysis and cluster analysis further revealed that the acorn sizes became larger and polyphenols became less with the increasing latitudes in both species. In North China, the acorns of Q. mongolica had small sizes and high polyphenols, which was contrary to those in Q. variabilis. These findings indicated that acorn traits were closely associated with the geographical distribution. Thus, our results will provide references for the selection breeding of acorn with the high starch, high or low polyphenols in the different regions.