In order to meet the requirements of miniaturization and lightweight development of T/R module in active phased array radar, the vertical interconnection model of ball grid array (BGA) is established with HFSS, and the influence of key structural parameters on transmission performance is analyzed, including solder ball radius, solder ball center distance, anti-pad radius of ground plane, pad radius, etc. Two types of three dimensional substrate stacked structures with different input-output (I/O) modes are designed according to application scenarios. The results show that increasing the radius of solder balls, decreasing the center distance of solder balls and choosing proper anti-pad radius are beneficial to the formation of good microwave transmission performance. The influence of pad radius is weak. Moreover, the return loss is better than 22.5dB, and the insertion loss is better than 0.13dB in X-band, after the vertical interconnection structure is optimized. The two types of substrate stacked structures both achieve good transmission performance, and meet different application scenarios and connection forms. Meanwhile, they can effectively realize the miniaturization of the module.