Abstract: Strong-motion observation records serve as direct evidence for investigating site effects. Based on the strong-motion data from the 2021 Yangbi Ms6.4 earthquake sequence in Yunnan Province, this study systematically examines local site effects on ground motions using both reference-site and non-reference-site methods. The research compares amplification effects between target soil sites and reference bedrock sites at different frequencies, revealing non-uniform amplification characteristics of linear site effects through ground motion regression residuals and identifying nonlinear site response features under strong shaking. The key findings are: 1) Surface soil layers exhibit significant amplification effects within the 1-10 Hz frequency band; 2) While Standard Spectral Ratio (SSR) and Horizontal-to-Vertical Spectral Ratio (HVSR) show excellent agreement in determining predominant frequencies of soil sites, HVSR exhibits systematic bias in estimating actual site amplification factors; 3)The linear site effects exhibit significant frequency-dependent characteristics, demonstrating non-uniform amplification patterns across different period ranges with particularly strong amplification effects within specific period bands; 4)Distinct nonlinear site response during the mainshock is evidenced by downward shifts of predominant frequencies in HVSR curves compared to aftershocks, a phenomenon corroborated by SSR analysis. These findings provide crucial insights for advancing the understanding of site effects and their influence on ground motions, as well as for engineering seismic design.