The crystal structure of the spin dimer magnet NaCu2VP2O10 was determined using single-crystal X-ray diffraction and electron diffraction. NaCu2VP2O10 displayed a non-centrosymmetric orthorhombic C2221 structure with a = 6.13860 (10) A, b = 14.4846 (3) A and c = 8.2392 (2) A. The layered structure comprised CuO4 plaquettes, VO6 octahedra and PO4 tetrahedra. A pair of CuO4 plaquettes formed Cu2O6 structural dimers through edge sharing. The Cu–Cu network formed a distorted puckered-layer structure with pseudo-one-dimensional characteristics. Maximum magnetic susceptibility was observed at ∼60 K and NaCu2VP2O10 became non-magnetic upon further cooling. The spin gap between the spin-singlet non-magnetic ground state and triplet excited state was estimated to be 43.4 K. Thus, NaCu2VP2O10 was assumed to be an alternating chain system with a singlet ground state of dimer origin. The V5+ ions in the VO6 octahedra showed large off-centre displacements along the [110] direction in the primitive perovskite structure, which were attributed to the pseudo-Jahn–Teller distortion of d0 transition metals.