This study was carried out to determine F1 single cross maize hybrids in four crop growing seasons (2010-2012) developed from the four maize inbred lines. Morphological traits and physiological parameters of the twelve maize hybrids were evaluated with the express goal to: (i) construct seed yield equation and (ii) determine grain yield attributing traits of well-performing maize genotype for effective selection using a previously unexplored method of two-way hierarchical clustering. Our data showed that in seed yield predicting equation photosynthetic rate contributed the highest variation (46%). Principle component analysis data showed that the investigated traits contributed up to 90.55% variation in dependent structure (i.e., grain yield per plant). Based on these findings, we found that factor 1 contributed 49.6 % variation (P< 0.05) with primary important traits (i.e., number of leaves per plant, plant height, stem diameter, fresh leaves weight, leaf area, stomatal conductance, sub-stomata CO2 absorption rate and photosynthetic rate). The two-way hierarchical clustering results demonstrated that Cluster III had outperforming genotype, H12 (Sultan × Soneri) along with its most closely related traits (photosynthetic rate, stomata conductance, sub-stomata CO2 absorption rate, chlorophyll contents, leaf area and fresh stem weight).Our data shows that H12 (Sultan × Soneri) possessed the highest grain yield per plant under high temperature and low irrigation regime conditions, which are most likely to exist in arid and semi-arid climatic conditions, such as in Pakistan.