"Certainty" and "wisdom" are not only frequent topics in Buddhism, but also very important practice goals for the Buddhist. Buddhist practicing focuses on thoughts in mind; therefore, to attain "certainty" and "wisdom", Buddhism practitioners should understand the thought's operation of "certainty" and "wisdom" in mind. Sutra show that the thought's operations for certainty in mind are cessation, stillness, quiescence, mental equipoise; those for wisdom are observation,illumination, reflection, and knowing clearly. "The observation of thoughts in mind" from Padmasambhava is an important method which contains the mental processes of certainty and wisdom. By the practice of observing thoughts in mind, Buddhist can attain certainty and wisdom.