Millimeter-wave (MMW) 3-D imaging based on multiple-input-multiple-output (MIMO) radar has been widely studied due to its unique advantages in human security screening. However, more research has been done on the use of scanning 1-D MIMO array and the fast imaging methods that match them. This limits the rate of data acquisition and imaging speed to some extent. It is necessary to study frame rate imaging system as well as efficient imaging methods. In this article, a boundary-type MIMO array is designed, based on which an efficient frequency-domain imaging algorithm with sub-aperture is proposed. The proposed algorithm solves the target reflectivity function by dividing the uniform array into two sub-apertures and solving the echo signals of each sub-aperture separately. The final target reflectivity function is obtained by superposing all the solutions. Compared with the advanced RMA, FSA and FωK algorithms, the proposed sub-aperture frequency-domain imaging algorithm (SFA) does not require a large amount of zero-padding to satisfy the requirements of fast Fourier transform (FFT) in all dimensions. It greatly improves the speed of imaging and saves the space required for computation. We derive the theoretical formulation of SFA applied to MIMO array and analyze its computational complexity and phase error. Simulation and experiment verify the efficiency of the proposed SFA.