phase problem about transceiver of stratix ii GX

You are not the first to tackle this problem. A search of the forum will reveal other similar discussions. The problem I believe is that the individual transceiver channels actually have internal reset circuitry. The serializers are coming out of reset at different (random) times. I do not believe you have access to control this.

Protocols that require strict channel-to-channel skew requirements typically use bonding.

It sounds like you obviously have control of the receiver as well if you're able to tolerate a fixed skew. Can you implement dynamic phase alignment at the receiver?

Jake