This paper proposes an isogeometric boundary element method (IGBEM) to solve the electromagnetic scattering problems for three-dimensional doubly-periodic multi-layered structures. The main concerns are the constructions of (i) an open surface (between two layers) and (ii) a vector basis function with using the B-spline functions. Regarding (i), we considered an algorithm to generate a doubly-periodic open surface with the tensor product of the B-spline functions of any degree. Regarding (ii), we employed the vector basis function based on the B-spline functions, which was proposed by Buffa et al [1], and adapted it to the underlying periodic problems so that it can satisfy the quasi-periodic condition on the boundary of an open surface. The proposed IGBEM worked for solving some numerical examples satisfactorily and proved the applicability to plasmonic simulations.