As the main nitrogen fertilizer in China, urea shows high activity. After hydrolysis in soil, urea is easily lost through volatilization and leaching, resulting in a low urea utilization efficiency, a waste of nutrient resources, and environmental pollution. Using organic acids to modify urea can delay urea decomposition, enhance urea use efficiency. However, the combination and enhancement mechanism is unclear. In this study, two low-molecular-weight organic acids, citric acid and salicylic acid, were selected as additives and added to molten urea to obtain urea containing citric acid (CAU) and urea containing salicylic acid (SAU). The combination of these two organic acids and urea was characterized by using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), liquid chromatography-mass spectrometry (LC-MS) and other analytical technologies. The results showed that after the combination of citric acid and salicylic acid with urea, there was an enhanced primary amine vibrational peak at 3 348 cm^-1 of FTIR spectra, indicating the reaction happened on the primary amine of urea. The new carbon structure (—C_X) and nitrogen structure (—N_X) was separated from the XPS C(1s) spectra and the N(1s) spectra, respectively. These new structures led to the decrease of the carboxyl group in citric/salicylic acid and amide group of urea. In addition, the C—OH chemical bond breakage happened in the XPS O(1s) spectra. The above indicated a new substance formed through the reaction of the carboxyl group in citric/salicylic acid and the amide group of urea to form a new substance. LC-MS analysis showed that the dehydration reaction happened between the carboxyl group of citric acid/salicylic acid and the amide group of urea, and that the new substance was structured with O=C—NH—C(O)—NH₂ will be produced in CAU or SAU. Therefore, the results from the spectral analysis and other analytical technologies used in this study clarified the combination characteristics of low-molecular-weight organic acid and urea. This founds a basis for the study on the reaction mechanism of organic polymer and urea and provides new ideas for the selection of high-efficiency fertilizer synergists.