The present invention discloses a water intake pipeline structure passing through a soft foundation embankment below a flood level and a construction method. The water intake pipeline structure comprises: pipelines, a gate valve well, a concrete pipe bed, a high-pressure jet grouting pile continuous wall, cement deep mixing piles, geogrids, backfilling clay, a clay bound macadam and concrete key walls. After the embankment is broken and excavated to reach a pipeline embankment-passing design elevation, the cement deep mixing piles are fully disposed in a plum blossom type, and the high-pressure jet grouting pile continuous wall is disposed under the gate valve well. A plain concrete cushion layer, the gate valve well, the concrete key walls and the concrete pipe bed are poured, the water intake pipelines are installed, and the pipelines behind the gate valve well are wrapped with concrete. The geogrids are placed during clay backfilling, and layered soil filling is performed. An embankment top is restored by using the clay bound macadam. The gate valve well is provided with a gate valve, and an operating lever is connected onto the gate valve. The present invention further discloses the construction method of the water intake pipeline structure designed to pass through the soft foundation embankment below the flood level. The present invention can eliminate differential settlement of an embankment-passing section, cut off seepage channels in contact positions of the pipelines and the embankment body, and improve the anti-skid stability of an embankment slope, and meanwhile it is novel in structure and convenient to implement.