In order to identify the maize seedlings which contain pesticide residues of coating agent, the roots and leaves of maize seedlings were studied by Fourier transform infrared spectroscopy (FTIR) combined with principal component analysis (PCA). The uncoated and coated maize seeds were planted with the same conditions, and the infrared spectra of roots and leaves of these seedlings were tested for parallel control experiments. At the same time, the infrared spectra of coating agent and cellulose were tested for reference. The infrared spectra of roots and leaves of the seedlings whose seeds were coated by coating agent showed a peak of C—H bending vibration near at 1 384 cm-1, but the C—H bending vibration in the infrared spectra of roots and leaves of seedlings without coatings appeared near at 1 375 cm-1. Referring to the infrared spectra of cellulose and coating agent, it can be determined that 1 384 cm-1 originated from the coating agent. At the infrared spectra of roots, the absorption peaks of pesticide residues at 1 384 cm-1 are particularly evident, which are sharper than that at 1 375 cm-1. With the growth of maize plants, the relative intensity of the characteristic peak at 1 384 cm-1 in roots tend to decrease, which is due to the continuous transport of pesticide residues to the above-ground organs of seedling, resulting in the reduction of pesticide residues in roots. Besides the characteristic peaks at 1 384 cm-1 of pesticide residues, the amide II band also shows obvious shoulder peak at the infrared spectra of seedling leaves whose seeds are coated by the pesticide, and this shoulder peak is not observed in seedling leaves whose seeds are uncoated. The spectral analysis showed that the characteristic absorption peaks of pesticide residues are covered up by the strong absorption peaks of cellulose, and the characteristic absorption peaks of cellulose result in overlapping of spectral information and redundancy of data. Therefore, the PCA was used to mine the characteristic information in the spectra. In the score plot of principal component 1 (PC 1) and principal component 2 (PC 2) of the roots, the samples containing pesticide residues and those without pesticide residues are clustered into two groups respectively, the scatter points of the two types of samples do not overlap, and the correct recognition rate is 100%. Although the leaves containing pesticide residues and those without pesticide residues are also divided into two groups in the score plot of PC 1 and PC 2, a small number of samples are overlapped, and the correct recognition rate is 93%. The results demonstrated the feasibility of utilizing FTIR spectroscopy combined with PCA, as an objective and rapid method for identification of the maize seedlings containing residual coating agent.