Posterior nasal neurectomy (PNN) is a commonly employed surgical approach for the treatment of allergic rhinitis (AR). Due to its denervation effect on the nasal mucosa, PNN may potentially alter the motion and defensive capability of cilia. Previous research on the effects of neural regulation and denervation on cilia has been limited by the absence of a feasible in vivo evaluation method for assessing ciliary function. Utilizing a new system developed by our team for visualizing and analyzing ciliary motion in vivo, we analysed ciliary beat frequency and distance in vivo and histomorphological changes in a murine PNN and AR model. Ovalbumin, histamine and neurotransmitters (acetylcholine chloride, α receptor agonist and β receptor agonist) were applied to investigate the responsiveness and neural regulation of the nasal mucosa. Denervation resulting from PNN led to a reduction in nasal ciliary beat frequency (CBF) to 78% of the control, as well as diminished response towards allergens and histamine. Among neurotransmitters examined, α receptor agonists exhibited inhibitory effects on in vivo ciliary motion while acetylcholine and β receptor agonists demonstrated stimulatory effects. PNN did not affect the reactivity of in vivo cilia towards these neurotransmitters. PNN-induced denervation can reduce ciliary motion, potentially compromising the defensive capability of nasal mucosa. Neural regulation and the neurotransmitters involved have significant effect on ciliary motion.