This study introduces Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that uses micrococcal nuclease and long cross-linkers to achieve nucleosome-resolution chromatin organization mapping in plants. The method reveals fine-scale chromatin structures and enhancer-promoter loops in *Arabidopsis*. Key findings include: 1. **Chromatin Domain Boundaries**: Over 14,000 boundaries were identified, primarily associated with chromatin accessibility, epigenetic modifications, and transcription factors. 2. **Gene Transcription and Chromatin Domains**: RNA Polymerase II (Pol II) occupancy and transcriptional elongation were found to influence local chromatin domains, with stronger domains and boundaries observed in highly expressed genes. 3. **Chromatin Loops and Stripes**: Distinct chromatin loops and stripes were identified between super-enhancers and their target genes, providing insights into the regulatory mechanisms of distal cis-regulatory elements. 4. **Regulatory Factors**: Potential regulators of chromatin loops, such as MORC7, MED2, and SAS complexes, were identified. 5. **Application to Other Plants**: Micro-C-XL was successfully applied to rice and soybean, demonstrating its broad applicability in plant genomics. The study highlights the superior performance of Micro-C-XL in resolving fine-scale chromatin organization and its potential for advancing the understanding of 3D genome organization and transcriptional regulation in plants.This study introduces Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that uses micrococcal nuclease and long cross-linkers to achieve nucleosome-resolution chromatin organization mapping in plants. The method reveals fine-scale chromatin structures and enhancer-promoter loops in *Arabidopsis*. Key findings include: 1. **Chromatin Domain Boundaries**: Over 14,000 boundaries were identified, primarily associated with chromatin accessibility, epigenetic modifications, and transcription factors. 2. **Gene Transcription and Chromatin Domains**: RNA Polymerase II (Pol II) occupancy and transcriptional elongation were found to influence local chromatin domains, with stronger domains and boundaries observed in highly expressed genes. 3. **Chromatin Loops and Stripes**: Distinct chromatin loops and stripes were identified between super-enhancers and their target genes, providing insights into the regulatory mechanisms of distal cis-regulatory elements. 4. **Regulatory Factors**: Potential regulators of chromatin loops, such as MORC7, MED2, and SAS complexes, were identified. 5. **Application to Other Plants**: Micro-C-XL was successfully applied to rice and soybean, demonstrating its broad applicability in plant genomics. The study highlights the superior performance of Micro-C-XL in resolving fine-scale chromatin organization and its potential for advancing the understanding of 3D genome organization and transcriptional regulation in plants.