The Chinese Crested Tern Thalasseus bernsteini (CCT) is likely the most critically endangered seabird species in Asia. The Matsu, Penghu, Jiushan, and Wuzhishan Archipelagos along the China coastline, plus Yeonggwang County in South Korea, are the five areas where this species is currently confirmed to breed. According to census and historical data collected in the Matsu Archipelago from 2004 to 2017, there was an average of 10 ± 4 adult CCT individuals at the Matsu Islands Tern Refuge (MITR) during the breeding season. CCT nested only in association with Greater Crested Terns T. bergii (GCT) among seven protected islands in the MITR, and the numbers of observed breeding individuals of the two species were positively correlated (r = 0.59, P < 0.001). We used generalized linear models to examine the effects of chlorophyll-a concentrations in surrounding marine habitats, typhoon frequency, and in-season shifts in colony location on inter-annual variation in numbers of breeding individuals and productivity (chick:adult ratios) of both CCT and GCT at the MITR from 2004 to 2017. Average chlorophyll-a concentrations during July-August obtained from the MODIS satellite were positively correlated with the annual maximum number of GCT at the MITR, but not that of CCT. In addition, we found that nest abandonment events during early incubation at the mixed-species colonies were associated with in-season shifts in colony location and delayed nesting chronology, thereby extending nesting into the peak typhoon season during July and August. The effects of in-season colony shifts on nesting chronology and the additive effects of typhoons caused a significant decline in CCT breeding success during the study period. We propose more rigorous monitoring to ascertain the root causes of in-season colony shifts of terns and then determine possible solutions. Additionally, creating educational programmes to increase public awareness towards seabird conservation could prove beneficial.