Soil remediation is the key issue supported by the national government in the 14^th Five-Year Plan for Economic and Social Development of P. R. China, and also important for socially sustainable development. Phytoremediation might remove metals from the soil more effectively compared to other methods. As the dominant location of metabolism in a plant cell, protoplast can get respond greatly to the reaction signal to heavy metals, similar to that of the plant cell wall. Currently, it is also significant to further reveal the remediation mechanism and response signal between plant protoplast and heavy metals during the phytoremediation process, with spectral analysis methods than molecular diagnostic techniques. Calendula officinalis was obtained via pot experiments under lead/cadmium contaminated soil, and the protoplast sample was derived with differential centrifugation technology. Tessier's Sequential Extraction Procedure-Atomic Absorption Spectrometry (AAS) was applied to study lead/cadmium speciation variation. The X-ray diffraction pattern (XRD), Fourier transform infrared spectroscopy (FTIR), two-dimensional infrared spectroscopy (2D-IR) and X-ray photoelectron spectroscopy (XPS) were used to investigate the spectral characteristics of protoplast under different lead/cadmium contents. The results show: the exchangeable contents of lead/cadmium in protoplast are relatively low, and the contents of cadmium with different speciation change little under different lead/cadmium concentrations in soil. The representative peak located at 31.7° in the XRD pattern, the evidence of sodium chloride crystal, and peaks of Pb₅(PO₄)₃Cl and CdS could also be easily found. The dominant absorbance band in FTIR spectra appears at 3 510 cm^-1, caused by the vibration of —OH. The peak becomes complicated and moves to some extent, and functional groups of —OH and C=O show a preferential combination to lead/cadmium, indicated from 2D-IR spectra. The elemental binding energies of C and O vary during the reaction in XPS spectra. The binding energy of C(1s) increases, and C atoms involve in complexation. The moving peak of O(1s) suggests the reaction nature might be complex. The new peak of Pb(4f) is caused by the interaction of π electron and lead ions. The binding energy of Cd(3d) increases at higher lead/cadmium contents, and cadmium would lose electrons during the reaction. The achievements, together with the results related to metals and Calendula officinalis cell wall obtained previously, will play an important role in the theory and technological improvement of phytoremediation.