The agricultural wastes, including crop straw and livestock and poultry feces, contain huge energy, and their rational reuse plays a significant role in avoiding the squander of resources and the environment pollution. This paper addresses this important issue by using the emergy theory and the ecological footprint theory. This paper first estimates the total amounts of crop straw, and livestock and poultry feces in each of years in Fujian Province from 1997 to 2006, according to the yields of the dominant crops, including rice, other grain crops, soybean, peanut, rapeseeds and sugarcane, and the numbers of main kinds of livestock and poultry, including hogs, bull, sheep, poultry, and rabbit including two conditions of the livestock and poultry on hand and the slaughtered ones. The emergy theory is taken as the main analysis method in this paper, and the total amounts of crop straw and livestock and poultry feces in each year are transformed into emergy by transformity. The paper identifies five main ways of reusing and dealing with the agricultural wastes in Fujian Province in resent ten years, including their uses as domestic energy (as the raw material of producing biogas), as fertilizer for returning fields, as the base of edible fungus, others such as the raw material of industrial manufacture, even including the direct disposal of their untreated part. And the energy flow fig of the ways of reusing and dealing with the agricultural wastes in Fujian Province is drawn, then the above five ways are respectively calculated in the period from 1996 to 2007 by using emergy analysis method. Applying emergy theory and ecological footprint theory, the value of the ecological footprint of this five ways is estimated per year basing on this theory, and the value of corresponding ecological carrying capacity is also calculated at the same time, and lastly the analysis results of reusing and dealing with agricultural wastes in Fujian Province are obtained by comparing the ecological footprint value with the ecological carrying capacity value in each year from 1997 to 2006. The results shows that the annual average ecological footprint of the ways of reusing and dealing with the agricultural wastes is 0.963 hm2/ person in resent ten years in Fujian Province, and the annual average ecological carrying capacity value of the ways is 2.262 hm2 / person, and the average value of the ecological surplus of the ways is 1.299 hm2 / person per year. In this paper, the ecological surplus increased gradually from 1.04 hm2 / person in 1997 to 1.54 hm2 / person in 2006. It indicates that there is still much room in the reutilization of agricultural wastes in Fujian Province, and their full reutilization will greatly promote the agricultural development and the improvement in the agro-ecological environment. Especially the untreated part of the agricultural wastes should be reused fully, it will lead to the win-win situation of economic development and ecological conservation. Therefore the relevant departments should take some measures to ensure the full reutilization of the agricultural wastes in Fujian Province.