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Topological charges are typically manipulated by managing their energy bands in quantum systems. In this work, we propose a new approach to manipulate the topological charges of systems by engineering density zeros of localized wave excitations in them. We demonstrate via numerical simulation and analytical analysis that the winding number of a toroidal Bose condensate can be well manipulated by engineering the relative velocities between the dark solitons and their backgrounds. The crossing of relative velocities through zero makes a change in winding number by inducing density zeros during acceleration, with the direction of crossing determining whether charge increases or decreases. Possibilities of observing such winding number manipulation are discussed for current experimental settings. This idea may also be to higher dimensions. These results will inspire new pathways in designing topological materials using quantum simulation platforms.