Six countries involved in the main water resource areas in Africa area of the “Belt and Road” were selected as research areas. According to 2015 data of water resources, food, and energy, the evaluation method of single index quantification and multiple indices synthesis and poly-criteria integration was used to calculate the safety indices of water, food, and energy in the study area and the comprehensive safety index of 3 kinds of resources and analyze their safety degree. The results show that Egypts water resources are highly unsafe, its food is lightly unsafe, its energy is basically safe, and its comprehensive safety degree is lightly unsafe. Sudans water resources are lightly unsafe, its food is highly unsafe, its energy is basically safe, and its comprehensive safety degree is lightly unsafe. Eritreas water resources and food are lightly unsafe, its energy is extremely unsafe, and its comprehensive safety degree is highly unsafe. Djiboutis water resources are highly unsafe, its food and energy are extremely unsafe, and its comprehensive safety degree is extremely unsafe. Somalis water resources are basically safe, its food is highly unsafe, its energy is extremely unsafe, and its comprehensive safety degree is highly unsafe. Kenyas water resources are lightly unsafe, its food is basically safe, its energy is extremely unsafe, and its comprehensive safety degree is highly unsafe.