The work aims to study the removal mechanism of the protective agent in conductive ink, so as to provide a reference basis for reducing sintering energy and realizing accurate sintering of printed electronics. The molecular dynamics (MD) method was used to establish models for protective agents containing carboxylic acids and polymers commonly used in conductive inks, to calculate the interaction energy between protective agents and silver surface. According to the simulation results, the magnitude of the interaction energy was mainly related to the relative molecular mass of protective agent and the variety and quantity of functional groups. With the increasing relative molecular mass of the protective agent, the absolute value of the interaction energy became greater and the energy for sintering became higher. At the same time, a linear curve was fitted by the interaction energy between the protective agent containing even number of carboxylic acid and the silver surface, which could also predict the interaction energy between the protective agent containing different even numbers of carboxylic acid and the silver surface. Through the near-infrared sintering experiments on two flexible substrates such as coated paper, and polyimide (PI) film, it was clear that there existed two stages in the sintering process of conductive ink:removal of protective agent and the densification process, and the two stages were conducted in synchronous crossing. As the sintering temperature increased, the sintering process became fast. The removal mechanism of the protective agent in conductive ink is revealed, which is conductive to selecting a suitable protective agent when preparing conductive ink, thus achieving precise sintering and saving energy.