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We study the quasinormal modes (QNMs) of massless scalar perturbations to probe the van der Waals like SBH/LBH phase transition of anti-de Sitter black holes in five-dimensional (5D) Gauss-Bonnet gravity.It is found that the signature of this SBH/LBH phase transition is detected when the slopes of the QNMs frequency change drastically and differently in small and large black holes near the critical point.The obtained results further support that the QNMs can be a dynamic probe to investigate the thermodynamic properties in black holes.