A vertical pump structure is adapted to be mounted on a water cooling tank. The vertical pump structure comprises a pump casing, an upper shaft seal, a shaft and a lower shaft seal assembly. An upper annular flange and a lower annular flange are formed on an inner surface of the pump casing. A drain space is formed between the two annular flanges. A drain hole communicates with the draining space and an internal space of the water cooling tank. The shaft is inserted through the two annular flanges. Two gaps, which are formed between the shaft and the two annular flanges, are respectively sealed by the upper shaft seal and the lower shaft seal assembly. Therefore, even if the lower shaft seal assembly fails, the upper shaft seal can still prevent leaking fluid from polluting the work place.