It is well-known that coastal low-level jets (CLLJs) play an essential role in transporting heat, water vapor and pollutants. However, the CLLJ characteristics in the Pearl River Estuary have not been deeply revealed due to the lack of long-term observations. Based on the long-term observations from a wind lidar, we analyze the primary climatic characteristics of the CLLJs in the Pearl River Estuary and investigate their relationships with large-scale and local-scale synoptic systems. The results show that the CLLJs mainly appear during the flood season, with the most occurrence in May. The CLLJ occurrence during the flood season is mainly influenced by the large-scale north–south pressure gradient driven by the western Pacific subtropical high and terrestrial low-pressure systems. The occurrence of the CLLJs exhibits a distinct diurnal cycle with two different peaks in different seasons. One peak appears at nighttime, mainly during non-flood seasons. The other appears in the afternoon, mainly during the flood season. In the non-flood seasons, under the influence of cold air, the inertial oscillations triggered by the land–sea thermal contrast lead to CLLJ onset at nighttime in the Pearl River Estuary. During the flood season, the strong near-surface pressure gradient contributes to CLLJ onset in the afternoon, while the topography (blocking and passing) is more conducive to the occurrence of the CLLJs in the Pearl River Estuary. These findings reveal the formation mechanisms of the CLLJs over the Pearl River Estuary, thus providing a basis for further understanding the precipitation in the Pearl River Estuary and the occurrence of the CLLJs in other coastal areas with complex mountain ranges.