Ultra-dry storage, storing orthodox seeds at ambient temperatures with moisture contents below 5%, can maintain seed viability for long periods with low input. Optimum moisture contents for ultra-dry storage exist and vary substantially among different seed lots due to their differences in desiccation tolerance, which is associated with the accumulation of protective compounds. To study the relationship between moisture contents of ultra-dry stored species, seed composition and the free-radical scavenging activity (FRSA). Eleven seed lots of maize, wheat, pepper, peanut, Chinese cabbage, and cucumber were chosen and multiple stepwise regression analysis was applied. In general, analysis of the seed lots revealed that optimum moisture contents for highest seed viability are below equilibrium moisture at 13% relative humidity and 20°C. Nevertheless, seed composition differed significantly among species. Lipids, flavonoids and the FRSA were significantly negatively correlated with the optimum moisture content of ultra-dry stored whole seeds and accounted for 97.7% of the total variation in the optimum moisture content. Lipids had the highest effect (90.0%) on the optimum moisture content of ultra-dry storage, which is consistent with the previous results. The FRSA and flavonoids accounted for 4.8 and 2.9% of total variation of optimum moisture content of ultra-dry stored whole seeds, respectively. The FRSA and flavonoids were also significantly negatively correlated with the optimum moisture content for non-lipid fraction of ultra-dry stored seeds, and accounted for 74.1 and 15.3% of the total variation in the optimum moisture content, respectively.