Water transportation in plants has been an important issue in plant ecophysiology. The most popular theory of the mechanism about sap flow in trees is cohesion-tension (CT) theory. However, it is difficult to explain how negative pressure of several MPa can exist and the continuity of water can maintain in those vulnerable vessels. Moreover, the existence of embolism is also a challenge to the traditional CT theory. The tension measured by xylem pressure probe was far lower than the value predicted by the CT theory since the 1990s. Therefore, in this field, many researchers have carried out further and more comprehensive studies. In our review paper, the hypothesis of the CT theory and its scientific controversies were introduced. Several hot topics in this field were summarized, which included: (1) xylem embolism and its refilling mechanism; (2) disaccord values of xylem tensions between two methods measured by xylem pressure probe and pressure chamber and the possible reasons; (3) compensating pressure theory put forward by Canny; (4) inter-surface tensions, capillary forces in water transportation, turgor pressure in parenchyma cells, xylem osmotic pressure, as well as reverse transpiration in sap flows; (5) Aquaporins in the cytoplasm membrane of the parenchyma cell in phloem and the companion cells of vessels in xylem. These topics play important roles in the explanation of water transportation mechanism in plants and lead the research in this field to a molecular level.