How to set the default packaged window size(ship mode)?

You can copy your ./Saved/Config/Windows/GameUserSettings.ini to ./Config/DefaultGameUserSettings.ini. If you don’t have the GameUserSettings.ini you can e.g. use this:

[ScalabilityGroups]
sg.ResolutionQuality=100
sg.ViewDistanceQuality=3
sg.AntiAliasingQuality=3
sg.ShadowQuality=3
sg.PostProcessQuality=3
sg.TextureQuality=3
sg.EffectsQuality=3

[/Script/Engine.GameUserSettings]
bUseVSync=False
ResolutionSizeX=960
ResolutionSizeY=540
LastUserConfirmedResolutionSizeX=960
LastUserConfirmedResolutionSizeY=540
WindowPosX=-1
WindowPosY=-1
bUseDesktopResolutionForFullscreen=False
FullscreenMode=2
LastConfirmedFullscreenMode=2
Version=5