Ammonia, which has advantages over hydrogen in terms of storage and transportation, is increasingly expected to become a carbon-free fuel. However, the reduction of fuel NOx emitted from ammonia combustion is an unavoidable challenge. There is the report that two-stage combustion with parallel independent jets could achieve Low-NOx combustion under ammonia/methane co-firing conditions. In order to further improve NOx reduction, we experimentally evaluated the effects of secondary air nozzle parameters, such as nozzle diameter and nozzle locations, on combustion characteristics in two-stage combustion of ammonia/natural gas co-firing using parallel independent jets. As a result of the experiments under various secondary air nozzle conditions, it was found that under the conditions where NOx was significantly reduced, the peak temperature in the furnace was observed at 300–500 mm in the axial direction from the burner, and then the temperature decreased toward the downstream of the furnace. We assumed that this temperature distribution reflected the mixing conditions of the fuel and secondary air and estimated the combustion conditions in the furnace. It was confirmed that the two-stage combustion was effective in reducing NOx by forming a fuel rich region near the downstream of the burner, and the lean combustion of the unburned portion of the first stage combustion with secondary air. We confirmed that the low NOx effects could be achieved by two-stage combustion using independent jets from the same wall under appropriate combustion and air nozzle conditions.