Since 2013 when the Belt and Road Initiative was proposed, China and Indonesia have achieved serval progresses with a series of mature frameworks and protocols. The 21st Century Maritime Silk Road initiative is one of major top-level designs for China to strengthen international cooperation for pursuing mutual benefit. Indonesian geographical advantage is outstanding because it locates at the intersection of the designed two major lines of the 21st Century Maritime Silk Road. Global Maritime Axis concept is a key program for Indonesia's development focus changing from land to sea. The 21st Century Maritime Silk Road is highly compatible with the Global Maritime Axis. The deep docking between them will bring new opportunities to scientific and technological cooperation between China and Indonesia. Based on systematical reviewing the status quo of scientific and technological cooperation between China and Indonesia, this study investigates the key points of agreement between the two countries in strengthening scientific and technological cooperation. Moreover, this study explores several critical areas with potential for cooperation, including marine resource planning, industrial chain optimization, infrastructure risk prevention and control, and major natural disaster response. Furthermore, some proposals are presented to promote the cooperation, especially for the response to natural climate change and natural disaster, based on the principles of concertation, co-construction, sharing as well as policy orientation, livelihood needs, and scientific goal.