The development of a multifunctional noncontact manipulation method is desired in cell manipulation. In this paper, we theoretically study and experimentally demonstrate the method of cell manipulation based on swirl. We analyze the swirl flow field features and the cell manipulation mechanism. The swirl is constructed by jetting fluid through three microtubules, and the cells are manipulated using the low pressure of stagnation point and the constant vorticity in the flow field. The experimental results indicate that the cell can be trapped robustly using the stagnation point of swirl. Moreover, the cell rotates with the same angular velocity at any position of the swirl flow field, and the cell is transported along with the movement of the stagnation point. Finally, we extend the application of swirl to manipulate multiple cells. Overall, this method can achieve trapping, rotating, transporting, pairing and enriching for cells, which realizes multifunctional cell manipulation.