Focusing his research on photochemistry, Natarajan studied various areas  of the discipline such as polymer dynamics using fluorescence, flash photolysis studies using picosecond and femtosecond lasers and solar energy conversion. He demonstrated that micromolecular dye coatings of electrodes used in photoelectrochemical cells returned high current density. This led to his subsequent studies of solar energy conversion using chemically modified electrodes. He published his research in peer-reviewed journals including Nature, Journal of the American Chemical Society, Journal of Physical Chemistry A, Inorganic Chemistry and Chemical Communications for a total of 107 articles. He was granted patents for four of his findings. He mentored over 30 doctoral scholars and was associated with a number of journals as their editorial board member. He also was on a number of government committees including those of the Department of Science and Technology and the Council of Scientific and Industrial Research and delivered several featured talks and orations.