A study had been conducted in qualitative design employing phenomenology approach to examine the cognitive basis and the semantic structure of phenomena based reasoning of lower secondary school students in Ambon. The data of the study were collected by using a test. Phenomena stimulus of science was given to the informants in the form of cognitive basis and semantic structure of phenomena based reasoning. This study concluded that (1) the cognitive basis of phenomena based reasoning were orientation, inferential abstraction, and inferential affirmation; (2) students were able to analyze phenomena by using systematic cognitive framework only if they had complete information of the phenomena; (3) inference validity related to the cognitive basis is heavily determined by the phenomena analysis ability; (4) the general semantic structures in phenomena based reasoning were definitional and assertional; (5) the semantic structure complexity was determined too by the phenomena knowledge availability which was analyzed.