The study of think tank problems typically involves complex systems, such as the economy, society, and science and technology. These systems usually consist of a large number of elements with extremely intricate relationships. The internal components of the system and their interactions are nonlinear and self-organizing, while the interactions between the system and the external environment are complex. This not only makes many of the problems that arise in the system unexpected, but also renders the role of policy for the system more uncertain. The relationships formed during the development of the system bring multiple uncertainties to the system. In particular, with the advancement of time, progress in science and technology, changes in the environment, and the increasing levels of industrialization and modernization, the study of think tank problems involves more complex issues. Given that we cannot get the full picture of all issues, uncertainty is becoming more prominent. This chapter will analyze the uncertainty of think tank problems, including the connotation of uncertainty, the uncertainty of think tank problems and the Double Helix Methodology in Think Tanks, and the uncertainty analysis method for think tank problem, and summarize the role of the Double Helix Methodology in Think Tanks in the study of uncertainty in think tanks.