Objective: To boost the effectiveness of internal audits in proficiency testing (PT) within the pharmaceutical field by exploring a new method for evaluating internal audit effectiveness by contrasting the results of internal and external audits. Methods: Descriptive statistics and comparative analysis methods were utilized to thoroughly dissect the relevant discoveries from the internal audits of the proficiency testing provider (PTP) system at the National Institutes for Food and Drug Control during 2020-2024, and a detailed comparison was made with the external audit findings. Results and Conclusion: From 2020 to 2024, 48 nonconformities were unearthed in the internal audits, spreading across 13 elements, while 39 nonconformities were spotted in the external audits, covering 6 elements. Significantly, report and document control are the two prominent overlapping elements in the distribution of nonconformities between the internal and external audits. It is found that the internal audit plays a substantial role in daily management; yet, there are shortcomings in the audit of proficiency testing scheme design. The external audit results convincingly confirm the effectiveness of the internal audit in enhancing some elements, and a strong complementarity exists between the internal and external audits, thus offering vital directions for the subsequent optimization of internal audit work.