more than 10 percent of the holy Quran verses have implied to the different natural phenomena and some of their features.This matter results the special notice to know these scientific verses of the holy Quran and their types and also the bases of the inference and scientific reasoning from these verses. With the examination of theverses of the holy Quran, it reveals that mentioning these natural phenomena in the holy Quran is in the different types and styles. In some scientific verses, God Almighty has explicitly stated these natural phenomena and asked human being to think and be aware of them. In contrast, several other verses of the Quran have implicitly implied some types of the natural phenomena in the different styles and methods. Findings of this research which has been adopted based on the descriptive- analytic method show that in addition to the explicit verses of the holy Quran which have directly indicated the natural phenomena, several cases of the features of the natural phenomena have been expressed by the several implicit scientific verses. Of these implicit scientific verses, it can be implied the verses of Qisas (stories) in the Quran, the verses of oaths, the verses of the Simile and Mathal (Pl. amthal, usually a proverb, but also a maxim, adage, or aphorism), the verses of the happenings at the Doomsday time, the verses describe the psychic phenomena and the Qur’anic verses related to rulings (Ayat al-ahkam). But for any true and scientific conclusion and inference perceived from the scientific explicit and implicit verses of the noble Quran, additionally to the general principles of the exegesis, it is necessary to be considered the specific bases originated from the holy Quran and intellectual dialogue principles. This paper shows that the effective basics in inferring from the scientific verses are: no path for falsehood (batil) in the Quran and in other statement, the verses of the holy Quran being right and authentic and showing real, non-verbal accompanying qarineh (indication), absolute and certain knowledge for God’s words and actof wisdom (hikmah) and at the end, it is necessary the existence of causes for the managing and running affairs by God.