Maintaining genetic diversity and aggregate traits selection in medicinal plants improves selection efficiency and provides the flexibility to adapt environmental stresses. The present studies aimed at evaluating genetic variation and assessing efficiency of three selection index models based on relative economic values of traits and a ranking based method in 30 cumin accessions under drought and well-watered conditions in 2015 and 2016 years. Drought stress regime applied at the flowering stage of growth cycle. The best linear unbiased estimation values (BLUE) were used for aggregate genotype selection in a desired direction in the Smith-Hazel I (SMH-I) and II (SMH-II), and Pesek-Baker (PSB) indices. The three selection indices did differ in assigning relative economic values for traits tested in cumin. Best linear unbiased predictions (BLUP) were used to predict rank summation index values (RSI). Grain yield (GY) ranged from 183.07 to 379.99 kg/ha and from 430.07 to 942.26 kg/ha in 2015 and 2016 experiments, respectively. Of the accessions tested in 2015, 20 with top rankings for GY were selected for further validation in 2016. Selections in 2015 resulted in 7.1% for plant height (PH) to 165.7% for plant weight (PW) progress in drought treatment in 2016. Among the traits, PH, thousand grain weight (TGW) and harvest index (HI) showed low changes between the two moisture regimes. Plant height with high heritability and significant correlation with GY showed low variation over seasons and watering regime treatments and is suggested for indirect selection of GY. Analysis of drought susceptibility index (DSI) showed that Kashmar with low DSI had low genotype × environment interaction for GY. Grains per plant (GPP) and biological yield traits had the highest response to selection under drought stress. The SMH-II showed higher selection efficiency in both seasons. Zarand had top rankings for RSI among accessions for aggregate traits tested under drought conditions in both years. Our results showed aggregate genotype selection is a refinement of selection which incorporates information of individual genotypes with genetic and association of traits. Overall, the efficiency of SMH II which maximized genetic gains in a desired direction was higher than SMH I and PSB indices that helps to achieve breeding goals in an uncertain number of generations in cumin.