Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most important disease affecting yield of soybean (Glycine max (L.) Merr.). In China, among the main physiological races of SCN causing serious economic loss of soybean, HG Type 0 is the most widely distributed. Breeding SCN-resistant varieties is one of the safest and most effective ways to manage SCN. Soybean cv. Dongnong L-204 has a green seed coat and is a resource for resistance to SCN; however, the transcriptional variation and main molecular mechanism of resistance of Dongnong L-204 are not clear. We obtained 66.42 Gb of raw reads by using Illumina HiSeq high-throughput sequencing of Dongnong L-204. Transcriptional changes at Days 3, 7 and 10 after HG Type 0 stress are described. In total, 11 279 differentially expressed genes were responsive to HG Type 0 stress, including 6407 SCN-induced and 4872 SCN-suppressed genes. Gene Ontology analysis emphasised the important roles of the terms metabolic process, single-organism process, catalytic activity and binding under HG Type 0 stress. Among them, the terms related to extracellular matrix, extracellular region part, membrane-enclosed lumen, protein-binding transcription factor activity, and symplast and cell junction existed only in pairwise comparisons Day 7 vs Day 0 and Day 10 vs Day 0. KEGG enrichment analysis showed that metabolic pathway played an important role in the stress response to HG Type 0. Cellular processes, metabolism and organismal systems and other pathway-related genes increased significantly after 7 days. Transcription factor analysis showed that transcription factors such as MYB, AP2-EREBP, bHLH, WRKY and NAC may be involved in the anti-HG Type 0 response of Dongnong L-204. At the same time, few transient inducible transcription factors were found and more transient inhibited transcription factors in Dongnong L-204 in the early stage of HG Type 0 syncytial establishment. RT-qPCR was used to analyse expression of 10 genes closely related to the HG Type 0 stress response. The expression of GmWRKYX1 was >60 times higher at Day 10 after HG Type 0 stress than at Day 0. The WRKY transcription-factor family may play an important role in the resistance of Dongnong L-204 to HG Type 0 stress.