To study the physiological and morphological relationships of two clover species affected by herbicides, Pursuit experiment in a factorial based on randomized completely design with 3 replications at the Damavand in 2012. The first factor consisted of two species of Trifolium pretense L. and Trifolium alexandrinum L. and the second factor consisted of three levels of herbicide Pursuit (0, 0.5, 1 and 1.5 litr per hectares). The traits in the study included chlorophyll a, chlorophyll b, total chlorophyll, carotenoids, anthocyanin, flavonoids, ratio chlorophyll a to b, ratio carotenoids to total chlorophyll, dry matter, protein content and weeds destruction. Results showed that maximum response to herbicide on the percentage of protein in the leaves was recorded under 0.5 li/ha herbicide Pursuit treatment. The results showed that the correlation between the Chlorophyll a with chlorophyll b, total chlorophyll, carotenoids, and chlorophyll b whit total chlorophyll, carotenoids and total chlorophyll with carotenoids and carotenoids with the ratio of carotenoids to total chlorophyll, and dry matter with flavonoids are significantly related. The results of step-wise regression analysis showed that chlorophyll b and flavonoids had positive and the effect of protein content was reduced by dry matter, anthocyanin and ratio chlorophyll b to chlorophyll a.