The invention relates to a ceramic CSP packaging substrate structure comprising a first circuit layer, a middle layer and a second circuit layer, wherein the first circuit layer comprises a first substrate, and a plurality of through holes are formed in the first substrate; the middle layer comprises a second substrate, and a plurality of second through holes are formed in the second substrate; the second circuit layer comprises a third substrate, a signal panel arranged on the third substrate and a shielding plate; a plurality of third through holes are formed in the third substrate, and thethird through holes and the second through holes are arranged in a staggered manner. According to the ceramic CSP packaging substrate structure, the first through holes, the second through holes and the third through holes are arranged in the staggered manner, tin leaking during welding can be prevented, and the airtightness and stability of welding can be ensured; the signal adopts a three-polarity arrangement, and can be applicable to differential signal transmission and non-differential signal transmission; and a large shielding plate is arranged around the signal plate, so that the anti-jamming capability is enhanced, and signal transmission stability is ensured.