The purpose of this study is to investigate middle school students’ developmental process of explanatory hypothesis formulation and the factors that affect the process, in optics, particularly in light interference phenomena. A teaching model was developed how explanatory hypothesis was formulated using an analogical reasoning, revised, and elaborated through scaffolding. Young used analogical reasoning for formulating an explanatory hypothesis on interference of light, comparing with the beat phenomenon in sound at first, and comparing with the interference phenomenon occurring in water surface wave, later. He explored the beat phenomenon in sound and interference phenomenon in water wave to develop the principles of superposition and interference of waves, and then applied them to formulate his early hypothesis on interference of light. Through continued study, Young revised and elaborated his early hypothesis into the principle of interference. For this study, progressive development model of explanatory hypothesis through exploration of analogical phenomena was developed, being used on Young''s process of explanatory hypothesis formulation using analogical reasoning, and incorporating scaffolding strategy , so that students could develop their own explanatory hypothesis. Based on this model, an instructional program was developed. In the analogy of this program, the target phenomenon was the interference of light represented by <the pattern of laser image passed through a double-slit>, and source phenomenon was the interference of water wave represented by <the pattern of wave made by two source water waves passed through two small holes closely located>. Young used the latter phenomenon to explain the principles of interference, and praised it as the most accurate analogy. The subjects for the study were 62 8th grade (average age 14) students, who were divided into 13 groups according to their cognitive level investigated by GALT test tool. The research findings are as follows. First, it was found that there is a regular pattern in development of explanatory hypothesis of both two point source water wave phenomenon and the pattern of laser passed through a double-slit. The former process consisted of three regular pathways, and the latter two. Second, the effect of cognitive level was apparent in the hypothesis development process. However, it was also observed that students with inferior cognitive level formed scientific explanatory hypothesis in the second stage of the scaffolding, which was never observed in previous studies. Third, the scaffolding actually helped the students in forming hypothesis. Finally, students formed scientific explanatory hypothesis when they used analogical reasoning. In conclusion, the analogical reasoning is indeed a very powerful tool in formulating explanatory hypothesis for scientists and even for secondary school students as they were observed in Young’s hypothesis formulation in optics and in students’ spontaneous analogical reasoning to formulate the hypothesis about the relationship between light and sound or light and water waves.