The critical methods for the scientific discovery should include abduction and induction that Peirce named as ampliative (synthetic) inferences, as well as analogy and metaphor that did not mentioned by Peirce but were very favor by contemporary cognitive scientists. In the authors view, abduction, induction, analogy and metaphor are the methods to be used in search of and set up hypothesis, and deduction, explicative (analytic or deductive) inferences named by Peirce, can be used in validating that hypothesis. The study advocates that all logical processing is accompanied with psychological processes in humans cognition, therefore, all logics are psychological. The author indicates that every process of proof is abductive by tracing the inferences in philosophy, logic and mathematics in the western world since Socrates. The authors also illuminate the effects of abduction, induction and analogy in scientific discovery with some examples in modern sciences such as continental drift and plate tectonics, Big Bang Cosmology, and theorem-proving with Balcon machine. Especially, this paper analyzes carefully the characters of psychological logics such as deduction and abduction with a famous Wason selection task as example. Then, a discipline frame of cognitive logic will be created, while abduction would be placed into this new frame becomingly, belonged to a sub-discipline of cognitive logic, i.e., psychological logics. Finally, a model in psychologcical logics with three parallel channels and a serial channel will be set up. With this model, abduction, analogy and induction should be used in describing or even to finding hypotheses in scientific discovery, while deduction should be used in validating the hypotheses. This model is an integrative model based on the cognitive scientific comprehensions, which is more advanced than any other similar models and has stronger explanations for scientific discovery. With this model, the author will discuss some problems related with scientific discovery and get some meaningful conclusions in this paper.