We develop a novel immersed boundary (IB) method based on implicit direct forcing scheme for incompressible flows. The proposed IB method is based on an iterative procedure for calculating the direct forcing coupled with the momentum equations in order to satisfy no-slip boundary conditions on IB surfaces. We perform simulations of two-dimensional flows over a circular cylinder for low and moderate Reynolds numbers. The present method shows that the errors for estimated velocities on IB surfaces are significantly reduced even for low Reynolds number with a fairly large time step while the previous methods based on direct forcing failed to provide no-slip boundary conditions on IB surfaces.