Fish ecosystems perform ecological functions that are critically important for the sustainability of marine ecosystems, as well as for global food security. During the 21st century, significant global warming caused by climate change has created novel challenges for fish ecosystems that threaten the global environmental and human health. Here, we study a coastal fish community in Maizuru Bay, Japan, and investigate the relationships between fluctuations of sea temperature and fish biodiversity and abundance. The global increase of temperature from 2002 to 2014 reduces fish diversity, while some species become more abundant and that causes ecological productivity to grow exponentially. The fish community is analyzed considering five temperature ranges: ≤10° C, 10-15° C, 15-20° C, 20-25° C, ≥25° C. In order to infer bidirectional interactions between species, an optimal information flow model is introduced in this study. We detect interdependencies between species and reconstruct species interaction networks that are functionally different for each temperature range. Networks for lower and higher temperature ranges are more scale-free compared to networks for the intermediate 15-20° C range in which the fish ecosystem experiences a first order phase transition from a locally stable state to a metastable state. Species-specific analysis is conducted by calculating the link salience and total outgoing information flow. Native species whose abundance is distributed more uniformly have a higher total outgoing information flow, and are the reference species (nodes in networks) of the most salient links. These species play an important role in maintaining the fish ecosystem stability. Species diversity, total interactions and entropy of species abundance in the fish community grow with the increase of temperature. This work provides a data-driven tool for analyzing and monitoring fish ecosystems under the pressure of global warming or other stressors. Macroecological and network-based analyses are useful to formulate science-based and accurate fishery policy to maintain marine fish ecosystems stable and sustainable.