The periodization and dating of the late-period Dunhuang grottoes (including those from the late Cao, Shazhou Uyghur, Western Xia, and Yuan periods) have in recent years become both a focal issue and a major bottleneck in Dunhuang grotto research. Scholarly disagreements remain considerable, with some views even standing in complete opposition to one another. Why has such a situation arisen? A survey of existing scholarship suggests that four key factors underlie this problem: the chronological attribution of the green murals; the origins and development of Shazhou Uyghur art; the relationship between visitors’ inscriptions and grotto construction; and the relationship between the dating of unearthed materials from the Northern Section and the construction of Mogao Caves during the Western Xia and Yuan periods. Resolving these four issues is the key to removing the major obstacles to the periodization and dating of the late-period Dunhuang grottoes. Through careful analysis, it can be found that these problems are not complicated when approached from a scientific perspective. The much-debated green murals can be reasonably dated to the early Western Xia period; the relationship between Uyghur-style mural art and the green murals is in fact remarkably close; the large number of visitors’ inscriptions can only indicate the overall decline of the Dunhuang grotto complex and the terminus ante quem of the relevant grottoes; and the predominance of artifacts from the Western Xia, and especially the Yuan, unearthed from the Northern Section sufficiently demonstrates that large-scale grotto construction at Mogao had ceased by the Yuan Dynasty.