To evaluate the shrinkage rate of small cervical lymph nodes (SCLNs) at different levels in patients with nasopharyngeal carcinoma (NPC) treated with radiotherapy retrospectively. 96 adult patients with NPC who underwent intensity-modulated radiotherapy (IMRT) at our institution were analyzed and followed-up. Evaluation of the response (shrinking rate) of SCLNs was determined by the bidimensional tumor area. Binary logistic regression was conducted to explore the risk factors associated with the shrinking rate of SCLNs. Of the 96 patients included in this study, 1,194 SCLNs were identified. Among the SCLNs, 28.6% were level IIb and 21.3% were level IIa. SCLNs at level IIa (96.1%), tended to have a response effect of no change (NC) with shrinking rate <50% (odds ratio [OR]=0.007; 95% CI: 0.003–0.021, P=5.287×10^-25). Conversely, the most proportionate share of SCLNs for shrinking rate ≥50% (complete response (CR) or partial response (PR)) was observed at level IIb (67.2%) (OR=6.104; 95% CI: 3.267–11.407, P=1.420×10^-8). There was no significant difference of shrinking rate between irradiation doses of 60Gy and 63Gy. Most SCLNs at level IIa were not shrunk after radiotherapy. The irradiation dose of SCLNs at level IIa should be not more than 60Gy to reduce side effects.