Herein, an innovative deep‐learning architecture is proposed to enhance the sensing capabilities of a microelectromechanical system (MEMS) used in fluid dynamic applications. The MEMS sensor comprises a polyvinylidene fluoride flexible (PVDF) piezoelectric flag and a bluff body, with vortex generation influenced not only by the bluff body's geometry but also by the input fluid speed. As a result, mechanical vibrations are induced in the piezoelectric flag, leading to charge displacement and the generation of electrical voltage signals. Through the developed deep learning method, accurate extraction of wind speed and successful classification of turbulence are achieved. Experimental tests in a wind tunnel, involving various wind speeds and bluff body geometries, demonstrate the robust correlation between the extracted continuous manifold in Fourier spectra and wind speed. By incorporating a feed‐forward network alongside the autoencoder, wind speed information even under strong turbulence is extracted. Moreover, the deep learning method's ability to classify different bluff bodies, independent of wind speed, is investigated. The findings reveal a unique capability to fingerprint turbulence and distinguish them for various applications. This research showcases the potential of our deep learning‐based MEMS systems for enhancing fluid dynamic sensing and classification tasks.