Here we have developed an approach of three-dimensional (3D) measurement of magnetic moment vectors in three Cartesian directions using electron magnetic chiral dichroism (EMCD) at atomic scale. Utilizing a subangstrom convergent electron beam in the scanning transmission electron microscopy (STEM), beam-position-dependent chiral electron energy-loss spectra (EELS), carrying the EMCD signals referring to magnetization in three Cartesian directions, can be obtained during the scanning across the atomic planes. The atomic resolution EMCD signals from all of three directions can be separately obtained simply by moving the EELS detector. Moreover, the EMCD signals can be remarkably enhanced using a defocused electron beam, relieving the issues of low signal intensity and signal-to-noise-ratio especially at atomic resolution. Our proposed method is compatible with the setup of the widely used atomic resolution STEM-EELS technique and provides a straightforward way to achieve 3D magnetic measurement at atomic scale on newly developing magnetic-field-free TEM.