The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting important regulatory elements (transcription factors binding sites (TFBSs), CpG islands, Tandem repeats, and conserved regions) and transcription factors (TFs) in a promoter or a set of promoters in plants. In this release, 17,230 TFs were collected from 78 plant species. Since ChIP-seq became a powerful technique to explore the regulatory landscape in genome, genomic locations of TFBSs were captured from 662 public ChIP-seq samples by using uniformly data processing in this study. The 1,233,999 regulatory linkages were identified among target genes and 99 regulatory factors (TFs, histones, and other DNA-binding proteins) across seven species including A. thaliana, O. sativa, Z. mays, G. max, S. lycopersicum, G. hirsutum, and A. lyrata. Additionally, this new version increased 2,449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. Besides integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events. These enhancements included: (i) 1,107 experimentally verified TF matrices from literatures, (ii) visualization of protein sequence annotations (such as functional domains, secondary structures, post-translational modification, and variants, etc.), (iii) 3D structures of TFs and TF-DNA complexes, (iv) condition-specific co-expression networks of TFs and their target genes which were extended to four species. It is not only efficient to investigate critical cis- and trans-regulatory elements in plant promoters, but also reconstruct high-confidence relationships of TF-targets under a specific condition. Confidently, the PlantPAN 3.0 will be helpful for scientists to understand complicated transcriptional regulatory networks in plants.