Benthic bivalve clam (Meretrix meretrix) is one of the most important economic shellfish and widely distributed in the coastal tidal flats of China. The coastal areas of Jiangsu and Liaoning Provinces are natural nursing ground for clams, and the amount of clams had reached more than ten thousand tons in the history. However, due to overfishing, the fishery resources of clams generally decline. Understanding the growth process of M. meretrix in natural waters is of great theoretical significance and application value for the quantitative research on assessing the ecological capacity of M. meretrix. Because the matter circulation and the energy flow are complex in marine ecosystems, it is difficult to evaluate the dynamic growth changes of benthic bivalve clam in natural waters through experiments. A mathematical model, as a research tool, provides an effective tool for the study of shellfish growth in varied water environments. In this study, a new model of the clam, based on the dynamic energy budget theory, was constructed. The developed model was parameterized based on the physiological and ecological data of clam obtained in laboratory and field experiments, which were analyzed by linear and nonlinear regression methods. The relationship between shell length and wet weight of clam was verified based on the comparison between data observation and simulation. The change process of shell length and wet weight of soft tissue was simulated by using WHDEBSTD software, which was originally developed by the authors, in the field environment. The results show that the shape coefficient of the clam is 0.57, the Arrhenius temperature value is estimated to be 9278 K, and the volume-specific cost for structure value is 2056.3 J/cm³. The good agreement between measured and simulated results of shell length, total weight and soft body weight change can be found in earth pond culture of M. meretrix. The average correlation coefficient R² is about 0.996 and the average discrepancy between simulated and measured is 3.58%. In the coastal area of Rudong, the shell length and the soft body dry weight of M. meretrix were observed as 3.12 cm and 0.48 g in June, and the simulated value were 3.2 cm and 0.476 g, respectively, which indicate that the numerical model could reproduce the growth of M. meretrix in the natural sea. This study provides useful information for research on constructing the clam module in ecosystem model and evaluating the ecological capacity of clam in natural waters. However, some discrepancies can still be found between the simulated and the observed growth of clam, which might be caused by the difference between the sexes of the clam in terms of growth and the fact that the hibernation state of M. meretrix cannot be reproduced by the numerical model. Follow-up studies will focus on the sexual differences and the hibernation state of clams, so as to further improve the accuracy and stability of the model.