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In conjunction with global warming, the frequency and intensity of typhoons in the Pearl River Estuary region are increasing annually, and coastal cities are becoming more vulnerable to compound disasters triggered by upstream flooding, typhoons, and astronomical tide surges, seriously threatening the lives and properties of people in the delta region. Quantitative analysis of the degree of variability of each factor associated with a compound flood event and accurate assessment of the magnitude of the compound flood event strongly impact the efficacy of coastal city responses aimed at disaster prevention and damage mitigation. In this study, focused on the Pearl River Estuary area, the tide levels at Sanzao station, wind speeds at Macao station, and daily maximum the maximum daily flow at Sanshui and Makou stations spanning 30 years from 1988 to 2017 were used to characterize the flood magnitude, typhoon magnitude, and astronomical tide magnitude of compound flood events in the Pearl River Estuary area. Data were screened using the annual maximum method. Based on the generalized additive model (GAMLSS) and the time-varying copula function, the encounter combinations of composite flood events of different levels and their main controlling factors were investigated. The results show that: 1) the main factors influencing initiation and magnitude of composite flood events in the Pearl River estuary area are non-consistent sequences that display interdependence. The time-varying copula model constructed in this study is more suitable for studies of composite floods than the traditional constant parameter copula model. Copula models are most applicable to studies of the encountered characteristics of multiple elements contributing to compound flood events and are most in line with actual situations. 2) Compared with the joint return period of traditional constant copula parameters, the period of occurrence of typical compound flood events in the Pearl River Estuary from 1988 to 2017 continuously shortens with time, the probability of occurrence increases, and the probability of future occurrence of extreme compound flood events is strengthening. The trend in which the return period of compound flood events is shortening with higher grades is accelerating. 3) Compound flood events throughout the Pearl River estuary area are more affected by typhoons and astronomical tides and less affected by water flow. When the return period of the three factors is one in 5 years, water flow causes the smallest increase in the co-occurrence return period; i.e., the influence of astronomical tide and typhoon on the scale of upstream flooding, composite flood events of typhoon, and astronomical tide is proportionately larger. Thus, composite flood events in the Pearl River estuary area are mainly impacted by typhoons with higher wind speeds. When the return period of the three factors is one in 10, 20, and 50 years, the increase in the co-occurrence return period caused by flow changes the most; and when the return period of the three factors is one in 10, 20, and 50 years, the acceleration of the co-occurrence return period caused by flow is the largest. When the three factors have a larger return period, astronomical tide exerts proportionately greater influence on the scale of the composite flood event of upstream flood, typhoon, and astronomical tide.