Methods and apparatus of Inter prediction for video coding including affine Inter mode are disclosed. In one method, an affine MVP candidate list is generated, wherein the affine MVP candidate list comprises at least one inherited affine MVP derived from a neighbouring block set. Prediction differences of a current control-point MV set associated with the affine motion model are encoded using one predictor selected from the affine MVP candidate list at the video encoder side or the prediction differences of the current control-point MV set associated with the affine motion model are decoded at the video decoder side using one predictor selected from the affine MVP candidate list. In another method, the inherited affine MVP is derived by considering whether at least one of reference picture lists of said at least one neighbouring block includes one reference picture being the same as a current reference picture of the current block.