Ecological protection and remediation of mountains-rivers-forests-farmlands-lakes-grasslands are important components of ecological civilization construction and territorial space governance in the new era. Based on the pilot project of ecological protection and remediation of mountains-rivers-forests-farmlands-lakes-grasslands, "two rivers and four mountains", in Chongqing, this paper explores the scientific ideas of overall protection, systematic remediation, and comprehensive management of mountains-rivers-forests-farmlands-lakes-grasslands in Ridge and Valley Province, as well as the differentiated ecological protection and remediation patterns and measures of "mountains", "valleys", and "rivers". This study found that the special landform condition of Ridge and Valley Province determines elements of the ecosystem with the characteristics of large longitudinal difference and strong gradation. The ecological protection and remediation of mountains-rivers-forests-farmlands-lakes-grasslands should be considered in the context of "mountains-rivers-forests-farmlands-lakes-grasslands as bodies", which means that different models of restoration and governance should be implemented from top to bottom according to the altitude. Ecological protection and remediation of "mountains" is the pattern of "conservation of recovery", mainly environmental governance of mine geology, forest tending, and biodiversity conservation. Ecological protection and remediation of "valleys" is the pattern of "comprehensive improvement", mainly comprehensive land improvement and soil pollution remediation. Ecological protection and remediation of "rivers" is the pattern of "combination of prevention and treatment," mainly the prevention of geological disasters along the two rivers, water environmental protection, and island ecosystem governance. In the future, institutional and mechanistic innovations should aim to expand the ecological functions of land tickets, implement verification systems for natural resources, perform a comprehensive pilot of a compensation system for ecological and environmental damage, improve compensation mechanisms for ecological protection, and establish incentive and guidance mechanisms, forming a joint force of system governance of mountains-rivers-forests-farmlands-lakes-grasslands, as well as the long-term mechanism of ecological protection and remediation.