The surface area changes of 151 natural lakes over 37 months in the Yellow River Basin, based on remote sensing data and 21 meteorological indicators, employing spatial distribution feature analysis, principal component analysis (PCA), correlation analysis, and multiple regression analysis, identify key meteorological factors influencing these variations and their interrelationships. During the study period, lake area averages were from 0.009 km2 to 506.497 km2, with standard deviations ranging from 0.003 km2 to 184.372 km2. The coefficient of variation spans from 3.043 to 217.436, indicating considerable variability in lake area stability. Six primary meteorological factors were determined to have a significant impact on lake surface area fluctuations: 24 h precipitation, maximum daily precipitation, hours of sunshine, maximum wind speed, minimum relative humidity, and lakes in the source region of the Yellow River generally showed a significant positive correlation. For maximum wind speed (m/s), 28 lakes showed significant correlations, with five positive and twenty-three negative correlations, correlation coefficients ranging from −0.34 to −0.63, average −0.47, indicating an overall negative correlation between lake surface area and maximum wind speed. For maximum daily precipitation (mm), 36 lakes had 21 showing a positive correlation, indicating a positive correlation between lake surface area and daily precipitation in larger lakes. Furthermore, of the 117 lakes with sufficient data to model, the predictive capabilities of various models for lake surface area changes showcased distinct advantages, with the random forest model outperforming others in a dataset of 65 lakes, Ridge regression is best for 28 lakes, Lasso regression performs best for 20 lakes, Linear model is only best for 4 cases. The random forest model provides the best fit due to its ability to handle a large number of feature variables and consider their interactions, thereby offering the best fitting effect. These insights are crucial for understanding the influence of meteorological factors on lake surface area changes within the Yellow River Basin and are instrumental in developing predictive models based on meteorological data.