This study investigated the infection and temperature-dependent dynamics of nervous necrosis virus (NNV) in native clownfish species of Taiwan. NNV was detected for the first time in three cultured species—Amphiprion ocellaris, A. frenatus, and A. clarkii—confirming their susceptibility to the virus and indicating that NNV has entered the ornamental fish breeding system. Two tail-fin cell lines derived from clownfish were used to examine viral replication and immune gene responses under different temperature conditions. Results showed that NNV replicated most efficiently at 28 °C, was suppressed at 24 °C, and although infection was promoted at 32 °C in A. ocellaris cells, viral yield declined at later stages due to heat stress. In contrast, A. clarkii cells exhibited greater thermal tolerance and sustained higher viral loads. Gene expression analyses revealed that TNF-α was a heat-sensitive proinflammatory gene, while IL-1β was induced in response to increasing viral load. These findings suggest that rising seawater temperatures may elevate the risk and duration of NNV outbreaks. Future studies should extend surveillance to other coral reef fishes and compare immune gene sequences—such as conserved regions of TNF among groupers and A. ocellaris—to elucidate molecular mechanisms of infection and develop predictive systems for marine fish diseases under global warming.