Cadmium (Cd) is one of the most important heavy metals in the environment which has several effects on the morphology, physiology, and anatomy of plants. It is a mobile heavy metal that can be transferred easily into plants, thus entering into the human food chain. Chamomile (Matricaria chamomilla L.) as an important medicinal plant can uptake and accumulate Cd in its root and aerial organs. In this research, the effects of different concentrations of Cd (90, 180, and 360 μM) were investigated on the growth parameters, anatomical features, and enzymatic antioxidant activities in flowers of chamomile after 7 days of exposure. The content of apigenin, a flavone compound mostly synthesizing in chamomile flowers, was also analyzed after 72 h from Cd treatment. The results showed that all concentrations of Cd reduced the length and biomass of roots and shoots, the diameter of flowers, as well as the number of pollen grains in tubular florets, while increased trichome density on the florets. Cd-treated plants showed an increase in antioxidant enzymes, superoxide dismutase (SOD), and peroxidase (POX) activities. After 7 days of treatment to Cd major concentration, flowers accumulated Cd and enhanced the apigenin production with the increase of Cd contamination in hydroponic solution. This increase of apigenin is most likely due to its antioxidant and sequestering property as a resistance response to Cd excess.