Watershed ecosystems include various environmental elements such as mountains-rivers-forests-farmlands-lakes-grasslands. Therefore, systematic restoration of the watershed ecosystem is important for implementing General Secretary Xi Jinping's concept:‘The aggregation of mountains-rivers-forests-farmlands-lakes-grasslands is a community of life’. The Loess Plateau is an area with the most serious soil erosion in the world; therefore, exploring the theory and practice of ecosystem protection of typical watersheds in the Loess Plateau is important for realizing the construction of national ecological civilization. This study proposed four key concepts of watershed ecosystem restoration:1) ecological restoration combining macro-planning and local restoration; 2) coordination between the promotion of regional ecological function and social economic development; 3) transformation from local restoration to global production; and 4) gradual guidance from engineering management to natural recovery. These four key concepts were proposed based on the characteristics and existing ecological problems of typical watershed ecosystems in the Loess Plateau. This study took the middle and upper reaches of the Fen River in Shanxi Province as examples, and proposed the practical design of ecological protection and restoration projects for mountains-rivers-forests-farmlands-lakes-grasslands. Additionally, five ecological restoration zones (Guancenshan water and biodiversity conservation area, water ecosystem protection area, soil and water conservation ecological restoration area, Fen River upstream ecological conservation restoration area, and post-mining ecological restoration area) and their restoration missions in the middle and upper reaches of the Fen River were introduced. Finally, ecosystem protection and restoration experiences of the pilot project in the middle and upper reaches of Fen River were summarized and four suggestions were proposed for improving the ecological restoration system and technology of typical watersheds in the Loess Plateau. This study is expected to provide references for the restoration and protection of watershed ecosystem on the Loess Plateau and in the whole country.