The biomass of marine fishery resources fluctuates in time. Understanding the features of biomass fluctuations at different time scales can provide a perspective in investigating the impacts of relevant factors on biomass variations. Based on the anchoveta (Engraulis ringens) biomass time series from 1985 to 2021, this study used Complete Empirical Mode Decomposition with Adaptive Noise (CEENDAN) to extract anchoveta biomass fluctuations features at different time scales and evaluated their contributions to overall time series. Besides, the results were evaluated with El-Niño and La-Niña events under cross-correlation analysis because these events greatly related with the variations in anchoveta biomass according to previous studies. Results showed the CEEMDAN could decompose the anchoveta biomass time series into five Intrinsic Mode Function (IMF_i) and one residual (RES). Anchoveta biomass fluctuations were mainly under the control of its seasonal, annual (IMF₁) and inter decadal (RES) variations. RES was found to be associated with the regime shift in Humboldt Current ecosystem at Southeast Pacific Ocean. Cross-correlation analysis revealed El-Niño and La-Niña events could impact the anchoveta biomass fluctuations mainly at annual and inter annual scale. Sea surface temperature anomaly at Niño1+2 region (Niño1+2 index) was believed to play a more obvious role in tracking the anchoveta biomass fluctuations than Oceanic Niño Index. Higher values of the Niño1+2 index within 1.0-1.5 years might have a negative impact on the anchoveta biomass.