A 3D semiconductor device and a 3D logic array structure thereof are provided. The 3D semiconductor device includes an array structure, a periphery line structure and a 3D logic array structure. The array structure has Y contacts located at a side of the array structure. Y is within MN-1 to MN. Y, M and N are natural numbers. M is larger or equal to 2. The 3D logic array structure includes N sets of gate electrodes, an input electrode and Y output electrodes. Each set of the gate electrodes has M gate electrodes. The Y output electrodes connect the Y contacts. The M·N gate electrodes and the input electrode connect the periphery line structure.