Since 1992, China has established 18 border economic cooperation zones in the border areas to drive and incite economic opening up along the border areas, to promote open cooperation and institutional docking between neighboring countries, and to achieve mutual benefit and win-win results. After infrastructure construction, invitation of investment, innovation and setting example, the significant achievements in the border economic cooperation zone have been made, however, its further development has been restricted by management system, industrial system and business environment and so on. Under the background of overall opening up promoted by the Belt and Road at new era, the border economic cooperation zone should realize overall transformation and upgrading by the evolution from agency management to organizational city, by industrial system optimization based on sustainable development of resources-style industry, and by perfecting business environment through the carrier of the urbanization of border ports. Furthermore, the border economic cooperation zones with better conditions should actively explore the transformation and upgrading towards cross-border zones.