Objective The purpose of this study was to provide an updated estimate of the prevalences of different types of human papillomavirus (HPV) in females in Chaoshan District and to establish an internal quality control (IQC) method for excluding false-positive results in HPV detection by using the Levey–Jennings control chart. Method HPV types were detected in 23,762 cervical samples by using PCR membrane hybridization. The means and standard deviations (SDs) of the positive rates were calculated, the Levey–Jennings chart was plotted, and the rules for “out of control” and “warning” were established. A set of standardized IQC for HPV DNA tests was developed based on the values and Levey–Jennings charts. Result In 466 batches, the positive rate exceeded the 1 + 2SD rule 24 times, but there was no consecutive exceedance, which was considered “in control”. When the positive rate exceeded the 1 + 3SD rule 8 times with consecutive exceedance, it was considered “out of control”. Further examination revealed that detections showing “out of control” had an undesirable random error, indicating that contamination may occur due to improper operation. Conclusion This unique Levey–Jennings control chart is a practical method for eliminating false-positive results in HPV DNA detection and should be widely applicable in molecular diagnostic laboratories.