A remarkable flow deviation phenomenon exists in the S-shaped discharge passage of a slanted axial-flow pumping system. In order to reveal the characteristics and development process of the deviating flow, numerical simulation was performed for a 15° slanted axial-flow pumping system, and the deviating flow was measured on an experimental rig. The details of the deviating flow in the S-shaped discharge passage were obtained. A kind of “unwinding” flow structure similar to that of DNA in biology is found in the S-shaped passage. The special structure is characterized by a “single strand” in which original helical streamlines are almost straightened. The bulk speed of the fluids on the “single strand” on the left side of the passage significantly increases while the swirling strength and the kinetic pressure ratio decrease. Large scale Dean vortices at the passage bottom interact with high transverse energy gradient fluids at the passage top as water flows into the convex part of the S-shaped passage, which leads to the emergence of the “unwinding” structure. Reverse secondary flows further enlarge the scale of the Dean vortices as water flows into the concave part of the S-shaped passage, which results in the growth of the “unwinding” structure. With the development of the asymmetrical flow structure, an irreversible severe flow deviation problem naturally comes into being.