The edible flowers of marigold (Tagetes spp.) are cultivated for their aesthetic appeal and high utility as functional health food ingredients. Carotenoid and flavonoid contents in marigold petals highlight the importance of selecting the appropriate cultivar and its processing methods for their industrial applications. The comparative understanding of the effects of dry processing on functional components across different marigold cultivars is still lacking. Therefore, this study investigated functional compound changes in the dry processing effect on four marigold cultivars with distinct flower shapes (Durango, Inca) and colors (yellow, orange). The petals in hot air drying (HAD) with 30, 60, and 90 °C applications were analyzed for the measurement of their individual secondary metabolite contents, total phenolic and flavonoid contents, and antioxidant activities. In freeze drying (FD), the lutein content varied significantly based on flower color, exhibiting higher levels in cultivars with orange petals. Otherwise, the levels of quercetin derivatives displayed distinct differences based on varieties other than color, with Inca cultivars demonstrating higher levels of quercetin 7-O-glucoside (Q7G) than Durango cultivars. In HAD, the lutein levels show a tendency to increase above 60 °C regardless of the cultivar. The content of quercetin glycosides decreased, while the aglycone increased in HAD treatments, regardless of the temperatures. Correlation and PCA results highlighted the impact of phenol compounds on antioxidant activity. Overall, these findings underscore the significance of variety and color in determining the chemical composition and antioxidant properties of marigold flowers.