Biochemical and physiological traits are affected by environmental stresses and therefore the breeding of these traits will play an effective role in stress tolerance. In this study, hybrids of five S7 lines of maize in a 5 × 5 half-diallel design were investigated in order to study the combining ability of biochemical and physiological traits of maize at the Research Farm of Graduate University of Advanced Technology, Kerman, Iran during the 2017-18 crop year based on randomized complete block design with three replications. The results of analysis of variance by fourth Griffing's method showed that the general (GCA) and specific (SCA) combining ability variances were significant for protein, proline, sugar content, carotenoid, chlorophyll a, chlorophyll b and total chlorophyll traits. Therefore, the role of additive and non-additive effects was identified in controlling these traits. Protein, proline, chlorophyll a and total chlorophyll traits were more controlled by additive effects, whereas the carotenoid trait was more controlled by non-additive effects and the role of additive and non-additive effects in controlling other traits was almost equal. The KSC704-S7-11 line showed positive and significant general combining ability for most of the studied traits, suggesting this line can be used in breeding programs to improve and increase stress tolerance. In addition, P1 × P3 and P4 × P5 crosses showed the most positive and significant specific combining ability for proline, chlorophyll a, total chlorophyll and carotenoid traits; thus they can be considered as the best hybrids to improve and increase stress tolerance in corn.