Multidimensional integration and multifunctional component assembly have been greatly explored in recent years to extend Moore’s Law of modern microelectronics. However, this inevitably exacerbates the inhomogeneity of temperature distribution in microsystems, making precise temperature control for electronic components extremely challenging. Herein, we report an on-chip micro temperature controller including a pair of thermoelectric legs with a total area of 50 × 50 μm2, which are fabricated from dense and flat freestanding Bi2Te3-based thermoelectric nano films deposited on a newly developed nano graphene oxide membrane substrate. Its tunable equivalent thermal resistance is controlled by electrical currents to achieve energy-efficient temperature control for low-power electronics. A large cooling temperature difference of 44.5 K at 380 K is achieved with a power consumption of only 445 μW, resulting in an ultrahigh temperature control capability over 100 K mW-1. Moreover, an ultra-fast cooling rate exceeding 2000 K s-1 and excellent reliability of up to 1 million cycles are observed. Our proposed on-chip temperature controller is expected to enable further miniaturization and multifunctional integration on a single chip for microelectronics.