In this study, we develop chromatin-associated RNA sequencing with structural insights to analyze the structure of chromatin-associated RNAs (caRNAs) in Arabidopsis at the transcriptome-wide level and the single-molecule resolution, emphasizing their role in RNA 3’ end processing. We focus on the function of RNA structures during the 3’ end formation, a crucial step affecting RNA maturation and stability. By subjecting Arabidopsis to cold treatments, we observe the induced alterations in RNA structure and investigate their implications in 3’ end processing under cold stress conditions. We have identified a distinct structural RNA feature characterized by single-stranded regions associate the poly(A) site, closely associated with cleavage events. Using deep learning, we have meticulously mined for sequence and structural motifs correlated with cleavage rate. Integrating our findings with in vivo structural data of single RNA molecules, we explore how various structural conformations at 3’ end region can influence the cleavage rate. We employ mutations that modify the structure to validate their functional impact. Our study confirms the pivotal RNA structures that mediate alterations in cleavage efficiency, providing novel insights into the RNA maturation process, especially under the environmental stress of cold in Arabidopsis.