The concrete-filled steel tube (CFT) members made of noncompact/slender sections, experiencing complex behaviors such as local buckling, concrete confinement and slippage between the components, have been increasingly used in the practical engineering structures. However, few reliable design methods were available until the latest AISC 360-16, in which two types of methods are firstly provided. The first one uses P-M interaction curves with reduced or effective stiffness method while the second adopts effective stress-strain relationships based on the fiber section approach. The beneficial effects due to the restraint of steel tube have been implicitly considered in both of them. The first method approximately accounts for the member stiffness and employs the effective length method for stability design while the second method does not fully fulfill the requirements of direct analysis specified in AISC 360-16 as lack of consideration of slenderness effects and initial geometrical imperfections. This paper proposes a flexibility-based beam-column with member imperfections and incorporates the effective stress-strain models into the fiber section for direct analysis of noncompact/slender CFT members. The gradual change of member stiffness and the actual section capacity can be accurately reflected in the analysis process and as a result, the traditional effective length method is no longer required in the proposed direct analysis. It is also found that the initial imperfection of L/1000 is insufficient for CFT members. Some useful recommendations in line with AISC 360-16 are provided for practical design. Several experimental tests demonstrate the accuracy and robustness of the proposed method.