One of the advantages of using Rydberg atom arrays in quantum computing and quantum simulation is the capability of realizing an arbitrary pairwise coupling network of interacting atoms. In this thesis, the atom arrangement algorithm previously developed for two-dimensional arrays is reconstructed to apply for three-dimensional arrays, by adding a tunable-focus imaging system. As-constructed three-dimensional atom arrays are used to experimentally perform the quantum simulations of the quantum Ising Hamiltonians of up to six-vertex mathematical graphs. The time-evolutions of the many-body quantum wave functions are observed and Fourier-transformed to obtain the many-body eigenenergies of quantum Ising Hamiltonians of the many-body system being continuously deformed from one graph to the other. Furthermore, Rydberg quantum wires are proposed and implemented by using auxiliary atom chains, to experimentally demonstrate the non-planar graphs and high-degree vertex graphs, and applied to solve the maximum independent set problems.