The invention discloses a plant seedling culture matrix nutrition mother agent and application thereof. The plant seedling culture matrix nutrition mother agent comprises macro-elements, mesne-elements, micro-elements and rare earth elements; the macro-elements are nitrogen element, phosphorus element and potassium element; the mesne-elements are calcium element, magnesium element and sulphur element; the micro-elements are ferrum element, manganese element, copper element, zinc element and boron element as well as beneficial rare earth elements. The plant seedling culture matrix nutrition mother agent is simply prepared with low cost of finished products, and has the following functions: 1) facilitating nutrients absorption, guaranteeing the nutrient demand and nutrient balance supply before field planting in the period of young seedling and boosting the growth of the young seedling; 2) improving young seedling resilience capacity including anti-disease, anti-drought, anti-chilling and other capacities to achieve the aim of even and strong sprout; 3) continuously enhancing chlorophyll content and photosynthetic efficiency of crops; and 4) promoting root system to be developed and guaranteeing the nutrient absorption. The invention has significant economic value.