The wild stocks of large yellow croaker Larimichthys crocea and yellow drum Nibea albiflora have been depleted since the 1980. Although the Chinese government has put a lot of effort (e.g., implementing fishing ban and releasing artificially bred fish into naturally distributed sea areas) into restoring their natural resources, the restoration still fails to expectation. We speculate that the slow restoration may be related to the increasing ship noise near the spawning grounds of these two species of fish. To test the harmfulness of ship noise on the L. crocea and N. albiflora, in our previous study, we studied the impacts of ship noise on their behaviors, parallelly, in the present study, we focused on the impacts of noise on their immunophysiological responses. We designed two experiments. In the first experiment, the juveniles were exposed to 120 dB ship noise for only once, then the plasma physiological indices were monitored every 1 hr within 4 hr. In the second experiment, the juveniles were exposed to 120 dB noise twice a day for 30 days, afterwards, the growth, plasma immune indices and intestinal microbiota were analyzed. The results showed that stimulated by ship noise, the physiological indices of L. crocea and N. albiflora both increased sharply within 3 hr. After a month noise stimulation, the growth and immune indices decreased significantly, and the proportion of intestinal microbiota was seriously imbalanced, showing Vibrio and Pseudomonas were dominant and other genera's abundance was quite low, especially some common intestinal probiotics. In addition, we also found that N. albiflora may be more sensitive to ship noise than L. crocea in terms of the required duration of physiological indices recovering to unstimulated level, and growth. This study highlights that ship noise negatively affects L. crocea and N. albiflora, which is helpful for some departments taking measures to protect the natural resource of these two species of fish.