Arctic temperature is one of the most uncertain aspects of mid-Holocene (MH) climate change modeling, usually attributed to the different responses of different models to external forcing. However, in this study, we find that significant discrepancies (i.e., the noise is close to the signal in term of climate change) in the MH Arctic temperature changes can occur within the same model and for identical external forcing due to initial ocean condition perturbations. It is shown that initial ocean perturbations can affect the surface energy budget change through the uncertain cloud effect on shortwave radiation in boreal summer. The resulted uncertain change in summer surface heat flux alters the subsequent autumn and winter sea ice and contributes to significant differences in Arctic temperature via sea ice-albedo feedback. This study suggests that internal uncertainty of an individual model is a non-negligible source of overall uncertainty in simulating the MH Arctic temperature change.