The environmental perturbation on atoms is a key factor restricting the performance of atomic frequency standards, especially in the long-term scale. In this Letter, we perform a real-time noise distinguish (RTND) to an atomic clock to decrease the uncertainty of the atomic clock beyond the level that is attained by the current controlling method. In RTND, the related parameters of the clock are monitored in real time by using the calibrated sensors, and their effects on the clock frequency are calculated. By subtracting the effects from the error signal, the local oscillator is treated as equivalently locked to the unperturbed atomic levels. In order to perform quantitative tests, we engineer time-varying noise much larger than the intrinsic noise in our fountain atomic clock. By using RTND, the influences of the added noises are detected and subtracted precisely from the error signals before feeding back to the reference oscillator. The result shows that the statistical uncertainty of our fountain clock is improved by an order of magnitude to 2×10?15. Besides, the frequency offset introduced by the noise is also corrected, while the systematic uncertainty is unaffected.