A novel, highly selective, and compact filter with controllable transmission zeros (TZs) is proposed in this brief. The hybrid structure of the proposed filter is based on the substrate integrated waveguide (SIW) and microstrip line resonators. The negative magnetic coupling was introduced through a full-wavelength microstrip line resonator, and the additional TZ was added by the cross-coupling of indirectly connected resonators in the traditional box-like topology. Consequently, high selectivity is achieved with TZs located at both sides of the passband. The independent control of the left and right TZs can be realized by controlling the cross-coupling and external coupling. The proposed work achieves good performance, including sharp skirt characteristics, compact size, and low loss. As a validation of the concept and performance, a filter prototype designed following the procedure is fabricated and measured.