A high-performance integrator is one of the key electronic devices for reliably controlling plasma in the experimental advanced superconducting tokamak for long pulse operation. We once designed an integrator system of real-time drift compensation, which has a low integration drift. However, it is not feasible for really continuous operations due to capacitive leakage error and nonlinearity error. To solve the above-mentioned problems, this paper presents a new alternating integrator. In the new integrator, the integrator system of real-time drift compensation is adopted as one integral cell while two such integral cells work alternately. To achieve the alternate function, a Field Programmable Gate Array built in the digitizer is utilized. The performance test shows that the developed integrator with the integration time constant of 20 ms has a low integration drift (<15 mV) for 1000 s.