This paper uses the finite element method to explain the specific nature of numerical instability such as network dependence in the topology optimisation of engineering structures from the perspective of partial differential equations. Gaussian function filtering method reduces the global impact of local extremum on topology optimisation. Finally, the method is introduced into the topology optimisation of concrete gravity dams in hydraulic engineering, and the topology optimisation program is developed in conjunction with ANSYS software language to achieve the topology optimisation of building structures in hydraulic engineering from a technical perspective.