Objective: To evaluate the protective effectiveness (VE) of the acellular pertussis vaccine (aPV) against pertussis in children aged 2 months to 6 years. Methods: A test-negative case-control study was conducted among children aged 2 months to 6 years who sought medical care for cough and underwent pertussis nucleic acid testing at sentinel surveillance hospitals in Zhejiang Province in 2024. Cases were defined as those with positive pertussis nucleic acid test results, while controls were test-negative individuals matched 1∶1 based on propensity scores using the caliper matching method. Conditional logistic regression models were used to calculate odds ratios (ORs) and VEs. Results: Among the 658 participants, 31.76% (209 cases) tested positive for pertussis. After propensity score matching, 203 cases and 203 controls were included in the analysis. The VE of 1-2, 3, and 4 doses of aPV against pertussis was 52.46% (95%CI:-39.82%-83.84%), 65.22% (95%CI: 6.86%-87.02%), and 72.21% (95%CI: 34.33%-88.24%), respectively. For pertussis-related hospitalization, the VE of 1-3 and 4 doses was 80.95% (95%CI:31.38%-94.71%) and 86.79% (95%CI: 51.89%-96.37%). The VE for those who completed 4 doses of vaccination and had intervals of less than 2 years, 2 years, 3 years, and 4 years or more after vaccination were 91.15% (95%CI: 67.61%-97.58%), 84.70% (95%CI: 43.71%-95.84%),56.23% (95%CI:-47.58%-87.02%), and 49.92% (95%CI:-83.74%-86.35%), respectively. Conclusion: The VE of aPV against pertussis in children aged 2 months to 6 years increases with the number of doses administered, and it is more effective in preventing hospitalization due to pertussis. The VE declines rapidly over time after the last dose. It is recommended to follow the new pertussis immunization program for timely and full vaccination.