Disclosed are a glycosaminoglycan lyase having difficulty degrading CS-E and an encoding gene and the use thereof. The amino acid sequence of the glycosaminoglycan lyase is as shown in SEQ ID NO. 2, and the nucleotide sequence of the encoding gene of the glycosaminoglycan lyase is as shown in SEQ ID NO. 1. The specific activities of the glycosaminoglycan lyase on HA and CS-A, CS-C, CS-D and CS-E are 13.8, 7.2, 6.7, 5.9 and 5.3 U/mg, respectively, and lowly sulphated CS-E polysaccharides are used as substrates to prepare highly sulphated oligosaccharides with different degrees of polymerisation, and the prepared highly sulphated oligosaccharides can be used for combating tumour metastasis. The enzyme can also be applied to fields such as medicine and cosmetics and has broad application prospects.