With the increasing demand for multi-function and highly integrated space-borne microwave products, a three-dimensional heterogeneous integration based on special substrates and other systems-in-package has difficulty with meeting the requirements of high reliability in space. Through simulation, the thermal-deformation resistance of traditional interconnections meets the requirements of high reliability, but its transmission performance at high frequency is poor. Based on the above, a novel microwave horizontal coaxial transition structure with good thermal-deformation resistance and excellent microwave characteristics is proposed. The design formula of the structure is derived, and the basic size of the structure can be quickly calculated. The transition structure and a vertical matching structure can realize microwave interconnection by combining microstrip impedance transformation and gold-ribbon interconnection. The complex microwave circuit is laid out and partitioned in a three-dimensional way, and thus a space-borne microwave metallic system-in-package method based on high reliability microwave interconnections is implemented. A Ka-band receiving system-in-package is used as an example to carry out the actual test and validation. The better characteristics of the Ka-band receiving channel on the satellite are obtained, and its excellent reliability is verified by the temperature cycle and mechanical vibration test.