Air-jet vortex spinning technology has emerged as a prominent method in the textile industry, owing to its superior production speed and the distinctive properties of the produced yarn. Nevertheless, the physical and mechanical performance of vortex-spun yarns is critically depend on the complex synergy between production parameters and yarn linear density (count). Consequently, an in-depth investigation into the interaction of these variables is imperative to optimize the production process and ensure consistent quality in different yarn counts. The main objective of the present study is to investigate the effect of production speed, spinning draft and break draft (each at three levels) and yarn count (at two levels) on the physical and mechanical properties of airjet vortex yarns. For this purpose, in order to accurately investigate the effect of the main variables on yarn properties and reduce the number of samples, a fractional factorial experimental design was used. According to this experimental design, 18 yarn samples were produced using Autoairo1 airjet spinning machine in two counts of 30 and 36 Ne. In this study, the physical and mechanical properties of the produced yarns—including tensile strength at break, elongation at break, hairiness, and mass irregularity(CVm)—were evaluated and statistically analyzed. Additionally, using scanning electron microscopy (SEM), the structure of air-jet yarns and the configuration of wrapper fibers were examined. The results revealed that the investigated variables had differing effects on the two yarn counts. Furthermore, the results demonstrated that production parameters, such as spinning speed and spinning draft, have a direct influence on yarn structure, particularly on the distribution pattern of the wrapper fibers in the yarn structure. Production speed and break draft showed a significant effect at the 95% confidence level on the hairiness of the yarns, and with increasing production speed, hairiness showed an increasing trend. Also, spinning draft showed a significant effect on the breaking strength of the produced yarns, and a decrease in breaking strength was observed with increasing spinning draft.