Characterization of the stiffness of multiple particles trapped by tweezers-based force spectroscopy is a key step in building simple, high-throughput, and robust systems that can investigate the molecular interactions in a biological process, but the technology to characterize it in a given environment simultaneously is still lacking. We first characterized the stiffness of multiple particles trapped by dielectrophoretic (DEP) tweezers inside a microfluidic device. In this characterization, we developed a method to measure the thermal fluctuations of the trapped multiple particles with DEP tweezers by varying the heights of the particles in the given environment at the same time. Using the data measured in this controlled environment, we extracted the stiffness of the trapped particles and calculated their force. This study not only provides a simple and high-throughput method to measure the trap stiffness of multiple particles inside a microfluidic device using DEP tweezers but also inspires the application of the trapped multiple particles to investigate the dynamics in molecular interactions.