Magnetocardiography (MCG) using superconducting quantum interference devices (SQUIDs) is a new medical diagnostic technique measuring biomagnetic signals that are generated by the electrical activity of the human heart. Since the magnetic fields in MCG have a vector property, a 3-dimensional MCG system measuring all three vector components of the magnetic field is more useful for an exact spatio-temporal analysis than measuring only one or two components. However, if a 3-dimensional (3-D) MCG system is to be constructed, a large number of sensors are needed. The difficulties in manufacture and maintenance will increase in proportion to the number of sensors. In this study, we assume a partial 3-D measurement system for which the number of sensor is fewer than it is for a full 3-D measurement system to find an optimal sensor array and to investigate the performance of the partial 3-D system with three different computer simulations focused on the spatial resolution and the localization reliability. In addition, we compare the performances of two different partial 3-D measurement systems with the performance of the full 3-D measurement system. Through the simulations, we confirm that the suggested partial 3-D systems show performances comparable to that of a full 3-D system even though the number of sensor is reduced.