Abstract: The structure of the fruit and seed, the multiple cotyledons in the seed embryo and their diversity characteristics of the rare and ancient plant of Malania oleifera, which is unique to China, have been studied deeply in terms of morphological anatomy and comparative development. The morphological and anatomical characteristics of the fruit and seed structure of M. oleifera have been revealed, and the diversity and regularity of the cotyledons in the seed embryo of M. oleifera have been discovered for the first time, and from the anatomical point of view, it is explained that the seeds of M. oleifera are physiological afterripening seeds and can not germinate in time. The results showed that the pericarp and seeds of M. oleifera accounted for 58.52% and 41.47% of the fresh weight, 27.0% and 73.0% of the dry weight of the fruit, respectively; the fresh weight of seeds is 12.48–29.61 g, which is composed of seed shell, endosperm and embryo. They account for 29.57%, 70.41% and 0.022% of the fresh weight of seeds, and 20.71%, 79.29% and 0.006% of the dry weight of seeds. Therefore, the seed embryo is very small and the endosperm is rich. The seed embryo consists of cotyledons, plumule, hypocotyl and radicle, but the number of cotyledons in the seed embryo varies from 2 to 5, and the number of cotyledons in the seed embryo with 3 and 4 cotyledons accounts for the vast majority(more than 87%), and the number of cotyledons in the seed embryo increases with the elevation of the distribution of M. oleifera. This is the first time to find the multi-cotyledonous and its diversity phenomenon in the seed embryo of M. oleifera, the multi-cotyledons and diversity of the seed embryo of M. oleifera were caused by the relatively primitive position and ancient characteristics of the angiosperm system at the early stage of the evolution of M. oleifera, rather than the natural variation or gene mutation under normal conditions. This discovery has important scientific significance and in-depth research value of M. oleifera in angiosperms.