The accurate detection of trace perfluoroalkyl acids (PFAAs) in drinking water remains challenging due to nonspecific adsorption losses during pretreatment. This study systematically evaluated the adsorption behaviors of 11 PFAAs across five filtration membranes and four solid-phase extraction (SPE) sorbents to establish an optimized analytical protocol. Results demonstrated that glass fiber (GL) filters minimized PFAAs retention (94.85% recovery in aqueous matrices) through electrostatic repulsion, outperforming other membranes such as polypropylene(PP). Among SPE sorbents, Weak Anion Exchange (WAX) exhibited the highest recovery rates among the sorbents evaluated (100.04% ± 2.74% recovery) via a dual adsorption mechanism combining amine-mediated ion exchange and hydrophobic interactions, achieving 30% higher efficiency than Hydrophile-Lipophile Balance (HLB) sorbents. The optimized method achieved low detection limits (LOD: 0.016–0.324 ng/L), high accuracy (spiked recovery: 80.12–115.76%) and precision (RSD < 10%). Method application revealed significantly lower PFAAs contamination in reservoir-sourced finished water compared to river/lake-derived supplies in the mid-Yangtze River region. This work effectively mitigates critical pretreatment biases in PFAAs analysis and provides a reliable solution to address the urgent need for monitoring PFAAs contamination in drinking water systems.