We propose a novel array of controllable double-well magnetic microtraps for cold atoms by using an array of square current-carrying wires and two additional bias magnetic fields. Arrays of double layer magneto-optical traps (MOTs) and Ioffe traps can be constructed by using same wire configurations and different currents and bias fields. Furthermore, the array of double-well magnetic microtraps can be continuously evolved as an array of single-well magnetic microtraps by reducing the currents in the wires. Our study shows that our scheme can be used to realize a controllable double-layer magnetic lattice with cold atoms, to form array of Bose-Einstein condensations (BECs), or to study atom interference, and so on.