Waste　recycling　has,　to　some　extent,　a　positive　effect　on　solving　resource　and　environmental　crises;　therefore,　it　has　become　an　important　measure　of　sustainable　development.　However,　the　resource　depletion　and　pollution　emissions　involved　in　recycling　and　manufacturing　processes　also　have　negative　impacts　on　nature.　To　solve　this　problem,　we　focused　on　the　waste　paper　recycling　system　in　order　to　build　an　ecological　costs　model　based　on　material　flow　analysis,　and　to　provide　a　basis　for　optimizing　the　waste　recycling　system.　In　this　paper,　we　define　the　concepts　of　ecological　costs　and　sum　up　the　existing　researches　on　these,　and　ensure　that　counting　ecological　costs　based　on　material　flow　analysis　is　practical.　Ecological　costs　are　cause　by　resource　consumption,　waste　emissions　in　the　processes　of　recycling,　manufacturing,　etc.　,　and　they　are　divided　into　the　three　categories:　resource　depletion,　environmental　pollution　and　protection,　and　ecological　damage.　Pollution　yield　and　environmental　protection　costs　are　counted　by　allocating　total　manufacturing　costs　into　positive　and　negative　products,　and　then　counting　resource　depletion　and　ecological　damage　costs　using　the　LIME　method.　Total　ecological　costs　in　the　recycling　system　are　calculated　by　summing　every　ecological　costs　in　the　whole　system.　Although　ecological　cost　accounting　is　an　important　means　of　evaluating　the　ecological　load,　the　constitution　of　ecological　costs　for　the　waste　paper　system　is　depicted　using　the　foundation　of　the　material　flow　chart.　The　model　we　built　is　not　only　fit　for　the　waste　paper　recycling　system,　but　also　valid　for　other　waste　products.　In　addition,　this　model　counts　the　ecological　costs　and　finds　out　the　manufacturing　progresses　with　high　ecological　impacts,　thereby　improving　them　and　providing　the　basis　for　both　environmental　and　economic　benefits;　thus,　it　constitutes　an　efficient　waste　recycling　system.　©　2017,　Ecological　Society　of　China.　All　rights　reserved.