Microfluidic chips represent a cutting-edge technology for manipulating fluids within micrometer-scale spaces and are gradually becoming a new favorite platform in life science research. Precise and fast zonal temperature control is essential for accelerating biological experiments. However, current multi-channel temperature controllers typically rely on multiple channel sets to achieve single set-point control, which results in discrepancies between the fluid temperature distribution and sensor temperature due to the distributed temperature field in the fluid channel. To estimate the actual temperature and implement gradient temperature control, this paper introduces an extension of the target tracking (TT) two degrees of freedom (2DOF) state feedback control (SFC) method, followed by a presentation of simulation and experimental results. Through comparisons with an enhanced PID system in both simulation and experimentation, the paper demonstrates an 8.96% reduction in the maximum temperature difference across different regions and a 27.89% decrease in the time taken to reach various temperatures. This solution effectively addresses the existing challenges in temperature control for microfluidic chips, offering a more precise and stable control within the desired temperature range.