We study the target space entanglement entropy in a complex matrix model that describes the chiral primary sector in N=4super Yang-Mills theory, which is associated with the bubbling AdS geometry. The target space for the matrix model is a two-dimensional plane where the eigenvalues of the complex matrix distribute. The eigenvalues are regarded as the position coordinates of fermions, and the eigenvalue distribution can be viewed as a droplet formed by the fermions, which is identified with one that specifies a boundary condition in the bubbling geometry. We consider states in the matrix model that correspond to AdS5× S5, an AdS giant graviton and a giant graviton in the bubbling geometry. We calculate the target space entanglement entropy of a subregion for each of such states in the matrix model as well as the area of the boundary of the subregion in the bubbling geometry, and find a qualitative agreement between them.