Ensuring food security is not only vital to the adequate supply of food in the world, but also the key to the economic development and social stability of various countries. Based on the panel data of 29 provinces in China from 2016 to 2020, this paper selects the number of foodborne diseases patients and iodine deficiency disease patients as reference objects, uses stunting rate of children under 5 years old, malnutrition rate of children under 5 years old, obesity rate of children under 5 years old, and newborn visit rate to measure improving nutrition, proposes Meta Entropy Two-Stage Dynamic Direction Distance Function (DDF) Under an exogenous Data Envelopment Analysis (DEA) model to measure the efficiency of hunger eradication, food security, and improving nutrition under the influence of exogenous variable rainfall. The research results indicate that the sustainability of China’s agricultural economy is insufficient, and the focus of attention should be different in different stages. In addition, the average efficiency of the three regions generally shows a decreasing level in the eastern, western, and central regions. In order to improve China's ability to guarantee food security, we must continue to strengthen the construction of agricultural infrastructure, increase policy support for green agricultural production, promote the diversification of agricultural production, and enrich people’s agricultural product consumption varieties.