Seed germination is among the most crucial and vulnerable stages in plant life cycles. Quercus marlipoensis is a critically endangered sclerophyllous oak endemic to the tropical montane cloud forests (TMCFs) of southeastern Yunnan, China. Only one population has ever been found, and it has shown regeneration difficulties. However, its seed biological traits and key restrictive germination factors remain unknown. In this study, we measured the seed biological traits of Q. marlipoensis and investigated the impacts of scarification, temperature, and water potential on its seed germination. We found that the seeds have typical epicotyl dormancy. Scarification by removing part or all of the pericarp and part of the cotyledon (1/3 and 2/3) increased the seed germination percentage. The seeds can tolerate low germination temperatures (Tb = 3.6°C), but germination occurred earlier under warmer temperatures (15–30°C) with T50 values from 2.1 to 3.4 days. Germination percentage, germination value, and germination index decreased linearly as water potential decreased from 0 to -1.0 MPa, while T50 increased. Quercus marlipoensis seeds are typically recalcitrant, and the germination percentage is highly sensitive to moisture loss. However, it can tolerate animal predation and low germination temperatures. Its germination traits are compatible with the unique limestone environment of TMCFs. The more frequent climatic extremes and droughts in recent decades in the Indo-China region have degraded its natural habitats. Therefore, ex-situ conservation by introducing seeds to nursery/botanical gardens and reintroducing seedlings into the native habitat is an efficient method to secure the survival of Q. marlipoensis in nature.