Abstract Because logical reasoning process and cognitive process exist simultaneously, science inquiry can not be separated from logical reasoning process. As the two ways of logical reasoning in cognitive process, induction and deduction play an important role in students' science inquiry activities, especially in the stage of raising questions, supposing, designing experimental program and explaining results. In this paper, the important effect of seeking-difference inductive reasoning in seeking for cause of phenomena, incomplete inductive reasoning in seeking for the common properties and change rules of chemical substances, deductive syllogism in searching for properties of single substance, and deductive explaining reasoning process in explaining single phenomenon in science inquiry.