Ecological security is receiving great attention in current researches, and the ecological footprint is one of the major methods in evaluating regional ecological security. However, few studies have determined the ecological footprint and ecological safety of a bay-type urban agglomeration using the improved ecological footprint method (EF-NPP). In this study, the Urban Agglomeration on Min Delta (UA-MD) was selected as a typical scenario, using NPP data as the real biomass, the regional ecological footprint and carrying capacity were measured with the regionalization of the yield factor denoted by "National Hectare". The ecological deficit and tension index were quantified, and the ecological safety of UA-MD during 2010-2015 was evaluated. The results showed that generally the ecological footprint of UA-MD rapidly increased between 2010 and 2015, especially in Quanzhou and Zhangzhou. However, the ecological footprint of UA-MD of Xiamen decreased slightly. In contrast, the regional ecological carrying capacity followed a decreasing trend, and most regions in UA-MD exhibited the ecological deficit phenomenon, with most serious in Xiamen, less serious in Quanzhou, and little changes in Zhangzhou. The ecological tension index of UA-MD continued to glow, and the ecological security level increased, which is consistent with the ecological deficit situation. Therefore, the ecological security problem needs to be solved urgently. The results may enrich case studies of ecological footprints and security, and provide valuable implication for the sustainable development of urban agglomeration.