Organic chemistry is the study of organic compounds containing hydrocarbons and their derivatives. It is similar to inorganic chemistry in terms of the cognitive model. However, the vast number of organic compounds has added to the difficulty in learning organic chemistry with compressed class hours in engineering majors. The integration of the process learning and reinforcement theories and organic chemistry content has led to a new notion, i.e., understanding and learning organic compounds with different functional groups in ionic reactions based on the acid-base theory. Thus, the organic chemistry content in the textbook was reorganized, and a three-stage teaching model including learning, learning transfer, and learning ability was designed. Comparative experimental results showed that the pedagogical scheme improved the learning efficiency of organic chemistry. In contrast, the learning process evaluation facilitated the learning acquisition transfer, innovative thinking development, and the high-quality growth of professional talent.