The　whole　finite　element　model　of　the　shielding　and　auxiliary　factory　structure　was　established　for　the　new　structure　of　nuclear　power　engineering　CAP1400,　and　modal　analysis　was　made　to　obtain　vibration　modes　of　the　nuclear　island　structure.Furthermore　the　effects　of　non-rock　sites　with　different　shear　velocities　on　seismic　responses　of　the　soil-structure　system　under　different　input　ground　motions　were　analyzed　by　the　finite　element　model　of　soil-structure　interaction.The　numerical　analysis　results　show　that　the　non-rock　site　makes　the　actual　input　ground　motion　of　nuclear　structure　foundation　a　significant　change;　The　response　acceleration　and　stress　of　nuclear　structure　foundation　increase,　but　the　response　displacement　and　the　period　corresponding　to　peak　spectral　acceleration　of　the　nuclear　structure　foundation　decrease　with　the　increase　of　the　shear　velocity　of　site.The　influence　of　non-rock　site　should　be　considered　for　the　nuclear　structure　seismic　design　because　of　soil-structure　interaction,　but　the　influence　may　be　neglected　in　the　case　of　the　shear　velocity　of　the　site　bigger　than　1　100m/s.　©　2017,　The　Editorial　Board　of　Journal　of　Basic　Science　and　Engineering.　All　right　reserved.