YMn6Sn6 consists of two types of Mn-based kagome planes stacked along the c-axis having a complex magnetic interaction. We report a spin reconstruction in YMn6Sn6 from ferromagnetic (FM) into a combination of two incommensurate spin spirals (SSs) originating from two different types of Mn kagome planes driven by frustrated magnetic exchanges along the c-axis with the inclusion of the Hubbard U . The pitch angle and wave vector of the incommensurate SSs are similar to 89 . 3 degrees and similar to (0 0 0.248), respectively, which are in excellent agreement with the experiment. We employ an effective model Hamiltonian constructed out of exchange interactions to capture the experimentally observed nonequivalent nature of the two incommensurate SSs which also explain the FM-SS crossover due to antiferromagntic spin exchange with correlation. We further report the existence of a topological magnon with spin-orbit coupling in the incommensurate SS phase of YMn6Sn6 by calculating the topological invariants and Berry curvature profile. The location of the Dirac magnon in the energy landscape at 73 meV matches with another experimental report. We demonstrate the accuracy of our results by highlighting the experimental features in YMn6Sn6.