Metamaterial leaky wave antennas (MTM-LWAs), one kind of frequency scanning antennas, exhibit frequency-space mapping characteristics that can be utilized to obtain a sufficient field of view (FOV) and reconstruct shapes in both remote sensing and microwave imaging. In this article, we utilize MTM-LWAs to conduct a spectrally encoded three-dimensional (3D) microwave tomography and remote sensing that can reconstruct conductive targets with various dimensions. In this novel imaging technique, we employ the linear sampling method (LSM) as a powerful and fast reconstruction approach. Unlike the traditional LSM using only one single frequency to illuminate a fixed direction, the proposed method utilizes a frequency scanning MTM antenna array able to accomplish frequency-space mapping over the targeted 3D background that includes unknown objects. In addition, a novel technique based on a frequency and polarization hybrid method is proposed to improve the shape reconstruction resolution and stability in ill-posed inverse problems. Both simulation and experimental results demonstrate the unique advantages of the proposed LSM using MTM-LWAs with frequency and polarization diversity as an efficient 3D remote sensing and tomography scheme.