As an environmentally-friendly technology attracting great attention from current researchers, phytoremediation is significant for site remediation contaminated by heavy metals. The plant will appear related physiological response to reduce direct harm caused by the stress of heavy metals. The microscale behavior is always multi-dimensional and difficult to detect. The advanced instruments are effective to resolve the scientific issues, while the related researches are seldom investigated. Taking calendula officinalis seedlings as experimental samples, scanning electron microscope (SEM) and Fourier transform infrared spectroscopy (FT-IR) were applied to compare the surface characteristics and functional groups variation, respectively. The response process and tolerance mechanism of calendula officinalis seedlings to lead and cadmium stress were further analyzed. The results showed: with the increasing concentration of lead and cadmium in loess, the calyptra of calendula officinalis seedlings become bending and wilting; the amount of root hairs decreases greatly while no significant variations of aerial parts are found on surface characteristics. The stress of lead and cadmium are responsible for the difference of FTIR spectra of Calendula officinalis seedlings. The peak absorbance at 3 573 cm-1 decreases and the peak becomes more complex with the increasing contents of lead and cadmium. It might be the coordination effect between lead/cadmium and hydroxyl, which affects the synthesis and secretion of organic matters. The movement of C—H vibration peak is associated with the lipid oxidationwhile the changes at 1 631 and 1 574 cm-1 suggest the protein component differences. The shifting peak at 1 385 cm-1 might be associated with the methylation of pectin and lipid, and the behavior is positive for the adaption process of calendula officinalis seedlings to lead and cadmium stress. The FTIR spectra are effective to reveal the phytoremediation mechanism on heavy metals contamination in pedosphere.