Iron deficiency has become a yield‐limiting factor in many agricultural areas. This study was conducted to elucidate the relationship between physiological traits and soybean [Glycine max (L.) Merr.] tolerance in the presence of different FeEDTA concentrations. Two hydroponic experiments using prescreened Fe‐efficient (FeE) and Fe‐inefficient (FeI) soybean genotypes were performed in 2014 and 2015, respectively. Various chlorophyll fluorescence parameters, antioxidant enzyme activities, and the dry weight of the plants were determined and analyzed by canonical correlation analysis, stepwise regression, and logistic equation. The effective quantum yield of photosystem II (PSII) (PhiPSII), maximal photochemical efficiency of PSII (Fv/Fm), superoxide dismutase (SOD), and peroxidase (POD) activity of the FeE genotypes were significantly higher than those of the FeI genotypes (P < 0.05). High catalase (CAT) and POD activities could improve photoprotection and PhiPSII under Fe deficiency. High POD and CAT activities and high Fv/Fm are conducive to increasing the chlorophyll content of E genotypes, and high CAT activity and longer ∆t are also conducive to increasing dry matter accumulation in FeE genotypes under Fe deficiency. In particular, in the presence of 0.02 mM FeEDTA, FeE genotypes exhibit higher PhiPSII, electron transport rate (ETR), and Fv/Fm values as well as higher SOD, POD, and CAT activities than FeI genotypes. Moreover, FeE genotypes show greater dry matter accumulation because of the longest ∆t in the presence of 0.02 mM FeEDTA. Thus, FeE genotypes have stronger tolerance to Fe deficiency because of their higher antioxidant, photochemical, and photoprotection abilities as well as their increased dry matter accumulation resulting from their longer ∆t in the presence of 0.02 mM FeEDTA.