Identification of soil components and soil organic matter characterization by functional group differentiation are the important applications of Infrared spectroscopy (IR) in which Fourier transform infrared spectroscopy (FTIR) is important. The objective of the study is to identify the FTIR spectrum of SOC changes by the changes of the carbon functional groups after the growth of rubber seedlings for a period of 8 months in three soils varied in pH and base cations. The study was conducted in the soils with three different pH viz. pH 4.4, pH 5.5 and pH 7.4. Each of these soils was collected in bulk quantity of about 600 kg each from three different locations viz. Malankara estate, Thodupuzha, TR & T estate, Mundakayam and large plantation in Wayanad. The influence of growth of rubber seedlings on changes in carbon functional groups were taken as the spectra of Fourier transform infrared spectroscopy (FTIR) in three different pH soil during initial and at 8 months. Results indicated that the spectrum of all three soils comprised of the clay mineral (left portion) organic matter (middle portion) and minerals (right portion) in the peaks obtained in three soils. The spectrum of the two acidic soil (pH 4.4 and pH 5.5) were similar and these were different from the neutral soil (pH 7.4). In the two acidic soils viz. pH 4.4 and pH 5.5, 6 peaks in the left portion were similar in manner. It is the determining factor for the presence of exchangeable cations like K, Na, Ca and Mg. These were the confirmation of the characteristic difference in pH 7.4 with variation in clay minerals particles along with high Ca and Mg content from the pH 4.4 soil and pH 5.5 soil. The sample used here was the rhizosphere soil after plant growth and the spectra changes by the changes in functional groups after the growth of rubber seedlings was very evident in pH 7.4 soil. The FTIR method is able to know the changes in SOC. The changes in SOC by the growth of rubber seedlings can be well identified by the changes in functional groups through FTIR Spectroscopy method. This is appropriate, accurate, beneficial as well as easy method and can be applied easily for soil carbon changes.