Porous mullite ceramics with an open/closed pore structure were prepared by protein foaming method combined with fly ash hollow spheres. Both the open porosity and total porosity of samples were enhanced by increasing the hollow sphere content. Mullite whiskers with a diameter of 0.2–4 μm were grown in-situ in the porous mullite ceramics with an AlF3 catalyst, conforming to a vapor-solid growth mechanism. The pore structure of the porous mullite ceramics was significantly affected by the mullite whiskers which increased the open porosity and total porosity. Moreover, the median pore size was reduced from 65.05 μm to 36.92 μm after the introduction of mullite whiskers. The flexural strength and the thermal conductivity of the samples decreased with increasing total porosity. The porosity dependence of the thermal conductivity was well described by the universal model, providing a reference for the prediction of thermal conductivity of porous ceramics with open/closed pores.