In the current study, we sought to track the clinical course of children under control-based asthma management and focused on respiratory pathogens monitoring. We prospectively explored influencing factors for asthma control. 121 children with uncontrolled asthma between 3-14 years of age were recruited. Common respiratory pathogens were detected with pharyngeal swabs and serum aeroallergen-specific IgE was measured. Numeric asthma control scores, airway resistance and fractional concentrations of exhaled nitric oxide (FENO) were evaluated. A proper control-based asthma management plan was established by the study physician. Regular reviews were performed, with the above measurements retested at set time intervals. The proportion of patients achieving asthma control at 1 month and 3 months were 59% and 76%; respectively (p=0.013). These patients exhibited significant improvement in numeric scores and lung function parameters. The prevalence of common respiratory pathogens did not significantly differ between reviews. The number of sensitized aeroallergens significantly increased with age (r=0.235, p=0.010). Children with a high visual analogue scale (VAS) score for asthma at baseline were less likely to achieve asthma control after 1 month, while those sensitized to more aeroallergens were more likely to achieve asthma control after 1 month (p=0.016 and 0.012). In summary, children with asthma showed significant improvements in control rates and lung function during control-based asthma management, independent of respiratory pathogens testing results. Patients with high VAS scores and fewer sensitizations to aeroallergens had difficulty achieving short-term asthma control.