The purpose of this study is to identify factors influencing fish production of shallow-sea aquaculture in South Korea. This study employed the two-way fixed effect and random effect models based on the panel models and also the difference between GMM and system GMM models based on the dynamic panel models using the amount of fish farming production, the number of stocked fry, the number of cultured fish, the amount of inputted feed, the farming area, the number of workers, and the sales price data from 2010 to 2017. First, the two-way fixed effect model of the panel models was selected by panel characteristics, time characteristics and Hausman tests and also the model was statistically significant. As a result of the two-way fixed effect model, the number of stocked fry, the amount of inputted feed, and the number of workers were identified as factors that increase the fish production of shallow-sea aquaculture. However, the number of cultured fish and the sales price were analyzed as factors that reduce the fish production of shallow-sea aquaculture. Second, the system GMM model of the dynamic panel models was selected by Hansen test and Arellano-Bond test in order to identify whether or not the over-discrimination condition is appropriate. Based on the system GMM model, the number of stocked fry, the amount of inputted feed, the number of workers in this year and 1 year ago, the number of cultured fish 2 years ago, and the sale price 3 years ago were analyzed as factors that increase the fish production of shallow-sea aquaculture. However, the amount of fish farming production 1, 2, 3 years ago, the farming area in this year, and the number of cultured fish in this year and 1 year ago were identified as factors that reduce the fish production of shallow-sea aquaculture. In conclusion, this study suggests that it is desirable to control the amount of stocked fry rather than to expand the farming area for fish farming in shallow-sea aquaculture, so as to keep the sale price at a certain level by maintaining the appropriate amount of fish production.