In the reentry process of hypersonic vehicles, unavoidable uncertainties can always crucially impact the trajectory performance. Therefore, even variable robust design algorithms have been proposed, both in areas of reference trajectory design and guidance algorithm design, effect analysis of the uncertainties still needs to be carefully taken. In this paper, a deviation condition strategy (DCS) is developed and applied to rank the uncertainty effects. In the proposed approach, given uncertainties are appended to open-loop control process regularly according to orthogonal experiment design, and the resulting system outputs are scientifically analyzed via a proper performance evaluation approach aiming at the order of uncertainty effects. In simulation, the methodology is illustrated utilizing a classic case of reentry vehicles. Compared with conventional methods, the proposed strategy significantly reduces the amount of calculation and evaluations. This work provides reference information about the uncertainties and will facilitate the robust design process somewhat.