To address the inherent contradiction between low-profile design and high gain in traditional omnidirectional antennas, as well as the narrow bandwidth constraints of ENZ antennas, this study presents a dual-mode ENZ-FP collaborative resonant antenna array design utilizing a substrate-integrated waveguide (SIW). Through systematic analysis of ENZ media’s quasi-static field distribution, we innovatively integrated it with Fabry–Perot (F–P) resonance, achieving unprecedented dual-band omnidirectional radiation at 5.18 GHz and 5.72 GHz within a single ENZ antenna configuration for the first time. The directivity of both frequencies reached 12.0 dBi, with a remarkably low profile of only 0.018λ. We then extended this design to an ENZ-FP dual-mode beam-scanning array. By incorporating phase control technology, we achieved wide-angle scanning despite low-profile constraints. The measured 3 dB beam coverage angles at the dual frequencies were ±63° and ±65°, respectively. Moreover, by loading the impedance matching network, the −10 dB impedance bandwidth of the antenna array was further extended to 2.4% and 2.7%, respectively, thus overcoming the narrowband limitations of the ENZ antenna and enhancing practical applicability. The antennas were manufactured using PCB (Printed Circuit Board) technology, offering high integration and cost efficiency. This provides a new paradigm for UAV (Unmanned Aerial Vehicle) communication and radar detection systems featuring multi-band operation, a low-profile design, and flexible beam control capabilities.