In this paper, a new formulation at the small time scale is proposed for multi-scale fatigue crack growth analysis and an in-situ SEM testing methodology is used to verify the basic hypotheses of the model. Very high resolution imaging analysis is performed to quantify the crack tip deformation behaviour and crack growth kinetics. In the in-situ SEM testing, the crack closure phenomenon is observed during the crack growth process. It is also observed that crack growth is not uniformly distributed within a loading cycle and only happens during a small portion of loading path. Based on the experimental measurement, the new prognosis model is developed and shows a good agreement with coupon level fatigue crack growth testing data under both constant loading and simple variable loading.