We use matrix model to study thermal phase in bubbling half-BPS type IIB geometries with SO(4)×SO(4) symmetry.Near the horizon limit,we find that thermal vacua of bubbling geometries have disjoint parts,and each part is one kind of phase of the thermal system.We connect the thermal dynamics of bubbling geometries with one-dimensional fermions thermal system.Finally,we try to give a new possible way to resolve information loss puzzle.