We studied the structural properties of (Ge+SiO2)/SiO2 multilayer films, especially the influence of the deposition temperature and the parameters of subsequent annealing on the formation and spatial correlation of Ge quantum dots in an amorphous silica matrix. We showed that in-layer and inter-layer spatial correlations of the formed Ge quantum dots strongly depend on the deposition temperature. For suitable chosen deposition parameters, highly correlated dot positions in all three dimensions can be obtained. It is demonstrated that the degree of the spatial correlation of quantum dots influences the size distribution width, which further affects the macroscopic properties of the quantum dot arrays.