Endometriosis (EMs) is a common gynecological disease with an increasing incidence in recent years. Because of the lack of specific molecular biological indicators in clinical practice, diagnosis is often delayed and the quality of life of patients is seriously reduced. Therefore, the discovery of effective molecular biomarkers is crucial for the early diagnosis and treatment of EMs patients. With the development of high-throughput sequencing technology, the mechanism of lncRNAs in EMs has been increasingly confirmed experimentally. This article summarizes the biological characteristics and functions of EMs-related lncRNAs, and introduces the mechanisms of EMs-related lncRNAs in the context of ceRNAs, in exosomes, under hypoxic conditions, and related antisense RNAs. The mechanism of the most popular imprinted gene H19 and metastasis-associated lung adenocarcinoma transcript 1 in EMs is then introduced. Finally, we explore the challenges of molecular biomarker EMs-related lncRNAs in the diagnosis and treatment of EMs, anticipating their potential value in clinical applications.