We measured plant traits and floral traits of Meconopsis integrifolia at different altitude populations (4 452 m, 4 081 m, 3 681 m), collected ripe fruits in the end of flowering and counted seed production per fruit to estimate the overall phenotypic selection differential and selection gradient. We used oneway ANOVA analysis to estimate variations of plant traits, floral traits and seed production per fruit at different altitude populations. We evaluated phenotypic selection (selection differential and selection gradient) on plant traits (plant height and leaf size), floral traits at different altitudes populations using multi linear regression model. The results showed that: (1) there were significant reducing of plant traits, floral traits and seed production with the increasing altitude. The higher altitude, the lower plant height, the smaller leaf size, the lower number of flower per plant, the smaller floral size and the lower seed production per fruit were in population. (2) We found significant differences on phenotypic selection of plant traits and floral traits at different altitude populations. In particularly, there were significant selection differential and selection gradient on number of flower per plant and floral size in population 3 (3 681 m); however, plant height, leaf size and number of flower per plant were more likely to be chosen in population 2 (4 081 m); interestingly, selection differential and selection gradient on leaf size and number of flower per plant were marginal significant in population 1 (4 452 m). (3) Our results indicated that divergent altitudes might lead to different phenotypes, floral traits were more likely to be chosen at lower altitude. By contrast, plant height and leaf size were more likely to be chosen because of rare pollinators and resources limitation at higher altitude.