In plant–pre-dispersal seed predator interactions (e.g., flowerheads–flies), insect morphological differentiation is frequently driven by divergent host plants. However, wing morphological variation among flies associated with different flowerhead species has seldom been explored in natural alpine systems. In an alpine meadow of the Qinghai–Tibet Plateau, larvae of four host-associated morphological groups of Tephritis sp. cf. femoralis (1, 2, 3, 4) feed on four asteraceous species: Saussurea nigrescens (SN), Carduus nutans (CN), Leontopodium leontopodioides (LL), and Anaphalis lactea (AL). We examined the wing size and shape of these four groups using a landmark-based geometric morphometric approach. The host plants vary significantly in capitular diameter, dry weight, and depth. Within each host-associated group, female wing sizes (length, width and centroid size) were significantly larger than those of males. Wing size differed significantly among the four female and four male groups across host plants. Female ovipositor length varied in parallel with capitulum depth across the four host plants. Significant intersexual differences in wing shape were observed in SN, LL, and AL. Wing shape also varied distinctly among groups in both sexes across host plant capitula, enabling clear discrimination of host-associated groups. Linear discriminant analysis achieved high correct classification rates for both sexes, supporting clear morphological separation among host-associated groups. In conclusion, variations in wing size, wing shape and ovipositor length were associated with host traits. Overall, our study illustrates morphological differentiation correlated with host plants in flowerhead–fly pre-dispersal seed predator interactions in the alpine meadow system.