Single-photon detection plays important roles in implementing desired quantum information processing. In this work, we propose a single itinerant photon detector based on absorption by two interacting atoms coupling to a waveguide, which can work in the microwave regime. Both the cases of giant and small atoms are considered. Each atom is modeled as a three-level system, with only one transition coupling to the waveguide. Our analysis reveals that, for a single atom coupled to the waveguide, the maximum detection probability is intrinsically limited to 0.5. This limit, however, can be lifted under perfectly chiral coupling, where unit detection probability becomes achievable. For the non-chiral case, we show that when a giant molecule consisting of two giant atoms with direct interaction couples to the waveguide, the single-photon detection probability can reach the ideal value of 1. Furthermore, we extend the model to the regime of small atoms and show that perfect single-photon detection remains attainable by appropriately tuning the direct coupling strength and the interatomic separation. These results provide a feasible route toward high-efficiency microwave single-photon detection based on engineered atom-waveguide interactions.