The invention discloses a construction method of shield continuous shaft crossing under the high-pressure-bearing water complicated stratum condition. The method comprises the following steps of: 1, end part reinforcement: reinforcing soil bodies at the shaft end part, and improving the self stability of the soil bodies to ensure the seepage flow avoidance; 2, tunnel face continuous wall breaking and removal and shaft refilling: breaking down and removing tunnel face concrete of a shaft layer by layer from bottom to top, clearing away waste concrete in the shaft layer by layer, and refilling the shaft by refilling materials; 3, shield tunneling and monitoring in a tunneling process; and 4, duct piece back grouting management: during shaft crossing tunnel exiting and tunnel entering of a shield tunneling machine, reinforcing the synchronous grouting by a shield tail before the tunnel exiting; inspecting the wall thickness grouting effect by a radar; determining whether secondary slurry replenishment is needed or not according to the wall thickness grouting effect; and ensuring the duct piece back filling compactness and the avoidance of water leakage towards a secondary lining shaft. The method has the advantages that the danger caused by high-pressure-bearing water complicated stratum condition during the shield shaft crossing is greatly reduced; the construction method is simple; the manufacturing cost is low; the shaft crossing speed is high; and the construction period is short.