This paper is devoted to solving a class of second order Hamilton-Jacobi-Bellman (HJB) equations in the Wasserstein space, associated with mean field control problems involving common noise. The well-posedness of viscosity solutions to the HJB equation under a new notion is established under general assumptions on the coefficients. Our approach adopts the smooth metric developed by Bayraktar, Ekren, and Zhang [Proc. Amer. Math. Soc. (2023)] as our gauge function for the purpose of smooth variational principle used in the proof of comparison theorem. Further estimates and regularity of the metric, including a novel second order derivative estimate with respect to the measure variable, are derived in order to ensure the uniqueness and existence.