PurposeThis meshless collocation method is applicable not only to the Helmholtz equation with Dirichlet boundary condition but also mixed boundary conditions. It can calculate not only the high wavenumber problems, but also the variable wave number problems.Design/methodology/approachIn this paper, the authors developed a meshless collocation method by using barycentric Lagrange interpolation basis function based on the Chebyshev nodes to deduce the scheme for solving the three-dimensional Helmholtz equation. First, the spatial variables and their partial derivatives are treated by interpolation basis functions, and the collocation method is established for solving second order differential equations. Then the differential matrix is employed to simplify the differential equations which is on a given test node. Finally, numerical experiments show the accuracy and effectiveness of the proposed method.FindingsThe numerical experiments show the advantages of the present method, such as less number of collocation nodes needed, shorter calculation time, higher precision, smaller error and higher efficiency. What is more, the numerical solutions agree well with the exact solutions.Research limitations/implicationsCompared with finite element method, finite difference method and other traditional numerical methods based on grid solution, meshless method can reduce or eliminate the dependence on grid and make the numerical implementation more flexible.Practical implicationsThe Helmholtz equation has a wide application background in many fields, such as physics, mechanics, engineering and so on.Originality/valueThis meshless method is first time applied for solving the 3D Helmholtz equation. What is more the present work not only gives the relationship of interpolation nodes but also the test nodes.