In-situ porous mullite ceramics with varying pore size and porosity were fabricated using 3D printing. The pore size was controlled by adjusting the size of polymethyl methacrylate (PMMA) microspheres. The effect of sintering temperature on phase evolution was also examined. Additionally, the impact of PMMA microsphere size and content on the rheological properties of the printing inks was investigated. The results indicated that alumina and microsilica fully transformed into mullite at 1550 °C. The influence of PMMA microsphere content and size on the porosity, mechanical properties, and thermal conductivity of 3D-printed porous mullite ceramics was also studied. The 3D-printed porous mullite ceramic prepared with 15 μm PMMA microspheres exhibited a porosity of 44.38%, a flexural strength of 58.53 MPa, and a thermal conductivity of 2.21 W/(m·K). This printing strategy offers a simple and effective method for fabricating porous mullite ceramics.