To design cross-coupled substrate integrated waveguide (SIW) bandpass filters (BPFs) with high performance, a new negative coupling structure is proposed, which is constructed by two coupled lines with shorted ends. The negative coupling structure is analyzed in detail. The stracture which can realize both relatively weak and strong negative coupling strength. The optimization method based on characteristic polynomials and reference zeros and poles of scattering parameters is realized for the filter design. To verify the proposed negative coupling structure, two fourth-order cross-coupled SIW BPFs with the center frequency of 10 GHz based on the optimized coupling matrixes are designed. The first one has a normalized bandwidth of 3% with a negative coupling in one cross-coupling path to illustrate the realization of weak negative coupling strength, and the second one has a normalized bandwidth of 8% with a negative coupling in one main coupling path to illustrate the realization of strong negative coupling strength. Finally, the two BPFs are fabricated and measured. Simulation and measurement results are in good agreement, which demonstrates the feasibility of the proposed negative coupling structure and its application on cross-coupled SIW filters with high performance. The influence of weak disperse cross coupling on locations of transmission zeros is also discussed.