The 2017 East Pacific Ocean Ecosystem Ecopath model was established and compared with that in 1997.The results showed that:the overall energy conversion efficiency of the ecosystem was 18.78%, indicating that the energy utilization efficiency had reached the optimal level. The evaluation of the ecosystem structure and function showed that the System Omnivory Index and the Connectance Index were 0.323 and 0.272, respectively. The indices indicated that the cohesion degree of the functional group and the complexity of the food web structure were low, which showed that the ecosystem in our study was susceptible to external environmental factors and fishing pressure. The ratio of total primary production to total spirometry was 2.593, which revealed that the ecosystem was immature. The total system flow, total biomass, and total circulation flow indicators were compared between the two phases, and the ecosystem scale and the food web complexity increased in 2017 and the maturity which was still in the development stage. It was assumed that there are uncertainties in the production statistics of large and small-sized individuals of yellowfin tuna and bigeye tuna. Three ecosystem models at different levels were constructed, which showed that the statistical error in production significantly affected our understanding of the ecosystem structure. Therefore, the trophic structure of different size groups and their impacts on the ecosystem should be fully considered.