We suggest a novel method to detect droplets and determine the protein content of droplets in microfluidic system using the 3ω method, which is a powerful tool to easily detect thermal response changes with a simple device. By measuring the thermal response of droplets and a carrying flow in real time, water droplets in an oleic acid carrying flow can be detected, and the concentration of bovine serum albumin in droplets can be estimated. This method is expected to increase the practicality and power of droplet-based microfluidic systems.