The relationship between internal fracture due to high-pressure hydrogen decompression and microstructure of ethylene-propylene-diene-methylene linkage (EPDM) rubber was investigated by atomic force microscopy (AFM). Nanoscale line-like structures were observed in an unexposed specimen, and their number and length increased with hydrogen exposure. This result implies that the structure of the unfilled EPDM rubber is inhomogeneous at a nanoscale level, and nanoscale fracture caused by the bubbles that are formed from dissolved hydrogen molecules after decompression occurs even though no cracks are observed by optical microscopy. Since this nanoscale fracture occurred at a threshold tearing energy lower than that obtained from static crack growth tests of macroscopic cracks (T (s,th)), it is supposed that nanoscale structures that fractured at a lower threshold tearing energy (T (nano,th)) than T (s,th) existed in the rubber matrix, and these low-strength structures were the origin of the nanoscale fracture. From these results, it is inferred that the fracture of the EPDM rubber by high-pressure hydrogen decompression consists of two fracture processes that differ in terms of size scale, i.e., bubble formation at a submicrometer level and crack initiation at a micrometer level. The hydrogen pressures at bubble formation and crack initiation were also estimated by assuming two threshold tearing energies, T (nano,th) for the bubble formation and T (s,th) for the crack initiation, in terms of fracture mechanics. As a result, the experimental hydrogen pressures were successfully estimated.