Mesona chinensis Benth. is a herbal plant with both edible and medicinal values. Thirty-four populations of M. chinensis in southern China were examined to quantify their morphological and phytochemical characteristics. The results showed that the populations differed significantly (p < 0.01) in each of the morphological and phytochemical characteristics. The morphological characteristics showed wide variation among populations, with CV values ranging from 15.76% to 54.18%. The herbage yield was mainly positively correlated with a number of stem traits. The cluster analysis showed that the populations belong to two major groups. Both total phenolic (TPh) contents and total flavonoid (TF) contents respectively ranged from 5.49 to 18.44 and 5.06 to 11.47 mg.g −1 among populations. Antioxidant activity, evaluated by means of ABTS (2, 2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid) and DPPH (1,1-diphenyl-2-picrylhydrazyl) assays, ranged from 63.91 to 223.41 and 30.35 to 137.84 mmol Trolox equivalents.g −1 , respectively, among populations. Significant positive correlations were found between antioxidant activity and TF contents, TPh contents, and total polysaccharide (TP) contents. Most of the 34 populations were rich in polysaccharides, while GD-6, GD-12, GD-3, GD-8, JX-6, and FJ-1 had the highest TP content in turn. Based on comprehensive grey correlation analysis, GD-1, GD-2, GD-8, FJ-6, FJ-3, FJ-2, JX-6, GD-7, JX-3, and JX-2 were the best performers for production and quality of M. chinensis in southern China.