Soil water content, matric potential, thermal properties, and electrical conductivity are fundamental and interrelated properties required by a variety of applications in soil science, hydrology, agriculture, and engineering. However, the measurements of the properties are affected by the temporal and spatial variability of soil due to employment of a variety of sensors, which hinders the research and modeling of coupled water, heat and solute transport. In addition, the laborious, costly and time-consuming sensor optimization is always a challenge for traditional sensor development. The objective of this study was to develop a multifunctional sensor integrating heat pulse, time domain reflectometry and porous ceramic matrix and optimize the sensor with COMSOL based numerical simulations. COMSOL simulated ceramic properties (e.g., thermal conductivity, volumetric heat capacity, dielectric permittivity, electrical conductivity) and soil properties (e.g., thermal conductivity and volumetric heat capacity) with different scenarios of sensor dimensions (e.g., the radius and length of the ceramic and extended rod length) were systematically evaluated and verified with experimental data. Our results show that the optimal radius and length of the ceramic are 18 mm and 40 mm, respectively, and the optimal rod length extended out of the ceramic is 50 mm. The optimized results indicate low estimation errors for dielectric permittivity (±1%), electrical conductivity (±1%), thermal conductivity (±2%), and volumetric heat capacity (±1%) of the ceramic as well as thermal conductivity (±3%) and volumetric heat capacity (±1%) of soil. The new multifunctional sensor can provide accurate measurement and modeling of soil hydrothermal properties.