A multi-layer modified trisection and its applications to substrate-integrated waveguide filters is presented in this article. By using source or load to replace a resonator of a conventional trisection filter, the multi-layer modified trisection could reduce one resonator but still reserves a transmission zero, which can be flexibly controlled either below or above the passband through adjusting the coupling manner and strength in the multi-layer structure. Moreover, based on low-temperature co-fired ceramic technology, the resonators in a multi-layer modified trisection can be embedded into ceramic substrate to achieve a more compact area. Two substrate-integrated waveguide filters are designed with a single transmission zero below or above the passband by introducing electric or magnetic coupling between the source and the resonator, respectively. Both are constructed by the multi-layer modified trisection. The impacts of coupling manner and level on the position of transmission zero are investigated and discussed. Furthermore, a cascaded multi-layer modified trisection filter with two transmission zeros in the lower and upper stopbands has been constructed by combining the two above-mentioned substrate-integrated waveguide filters. Two transmission zeros are controlled by two filters, namely, one by electric coupling and the other by magnetic coupling between source/load and resonator, respectively. Those filters have been fabricated in the low-temperature co-fired ceramic process. Measured results, which exhibit good selectivity and low in-band insertion loss, agree well with simulated ones.