Parameterization of computational domain plays an important role in isogeometric analysis as mesh generation in finite element analysis. In this paper, we investigate this problem in the 2D case, i.e, how to parametrize the computational domains by planar B-spline surface from the given CAD objects (four boundary planar B-spline curves). Firstly, two kinds of sufficient conditions for injective B-spline parameterization are derived with respect to the control points. Then we show how to find good parameterization of computational domain by solving a constraint optimization problem, in which the constraint condition is the injectivity sufficient conditions of planar B-spline parametrization, and the optimization term is the minimization of quadratic energy functions related to the first and second derivatives of planar B-spline parameterization. By using this method, the resulted parameterization has no self-intersections, and the isoparametric net has good uniformity and orthogonality. After introducing a posteriori error estimation for isogeometric analysis, we propose $r$-refinement method to optimize the parameterization by repositioning the inner control points such that the estimated error is minimized. Several examples are tested on isogeometric heat conduction problem to show the effectiveness of the proposed methods and the impact of the parameterization on the quality of the approximation solution. Comparison examples with known exact solutions are also presented.