<p>Improving the sensitivity of parasite detection is an urgent task for global public health. The traditional manual microscopy method still has some shortcomings in fecal parasite detection. This study aimed to evaluate the clinical application value of the KU-F40 fully automated fecal analyzer in fecal parasite detection by comparing the fecal detection results of the manual microscopy method with those of the KU-F40 instrumental method. Fecal test results were collected from January to June 2023 and January to June 2024, and divided into manual microscopy group (<i>n</i> = 51,627) and KU-F40 instrumental group (<i>n</i> = 50,606) according to methodology. The detection levels and species of parasites detected by the two methods were retrospectively analyzed. The KU-F40 instrumental group had a higher parasite detection level (8.74%) than the manual microscopy group (2.81%), with statistically significant differences between groups (<i>χ</i>² = 1661.333, <i>P</i> &lt; 0.05). Five species of parasites were detected by the manual microscopy method and nine species of parasites were detected by the KU-F40 instrumental method, of which the detection levels of <i>Clonorchis sinensis</i> eggs, hookworm eggs and <i>Blastocystis hominis</i> were higher than those of the manual microscopy method, with statistically significant differences (<i>P</i> &lt; 0.05). Although the detection levels of tapeworm eggs and <i>Strongyloides stercoralis</i> were also higher than the manual microscopy method, the differences were not statistically significant (<i>P</i> &gt; 0.05). The KU-F40 fully automatic fecal analyzer has a higher sensitivity to parasite detection and holds significant clinical application value in the detection of fecal parasites. With the combination of manual re-examination, the accuracy of test results can be significantly improved.</p>