日(ri)本有(you)(you)機(ji)生態農(nong)業最顯著的(de)特征是，首(shou)先，以追(zhui)求超高品質為目標，合(he)理負(fu)載，限制高產(chan)，減少土壤產(chan)出。其次(ci)，大力(li)發展堆肥，廣開肥源。以日(ri)本果(guo)園(yuan)(yuan)(yuan)(yuan)為例，一些果(guo)農(nong)發展起了畜牧業，保(bao)證果(guo)園(yuan)(yuan)(yuan)(yuan)有(you)(you)足量的(de)有(you)(you)機(ji)肥。日(ri)本幾乎(hu)所有(you)(you)的(de)果(guo)園(yuan)(yuan)(yuan)(yuan)都(dou)采用(yong)(yong)生草技(ji)術，不少果(guo)園(yuan)(yuan)(yuan)(yuan)還利用(yong)(yong)生物菌群，將生產(chan)蘑(mo)菇的(de)下腳(jiao)料和鋸末進行處理漚制，形成(cheng)有(you)(you)機(ji)肥施入果(guo)園(yuan)(yuan)(yuan)(yuan)，效果(guo)非常好。

眾所周知(zhi)，有(you)機(ji)質含量是土(tu)(tu)(tu)(tu)壤肥(fei)力(li)的重要(yao)(yao)指標，有(you)機(ji)質是土(tu)(tu)(tu)(tu)壤養分的主要(yao)(yao)來源，可促進土(tu)(tu)(tu)(tu)壤結構形成(cheng)，改善土(tu)(tu)(tu)(tu)壤物理性(xing)質，提高土(tu)(tu)(tu)(tu)壤的保肥(fei)能力(li)和緩沖性(xing)能，同時(shi)有(you)機(ji)質中(zhong)的腐殖(zhi)質具有(you)生理活性(xing)，能促進作物生長發育(yu)；有(you)機(ji)質中(zhong)的腐殖(zhi)質還(huan)具有(you)絡(luo)合作用，有(you)助于消除土(tu)(tu)(tu)(tu)壤的污染(ran)。

在日本(ben)，果(guo)(guo)園(yuan)有(you)機(ji)質含(han)量大多達(da)到了6.8%。有(you)人可(ke)能對這(zhe)個數(shu)字沒有(you)概念(nian)，舉個例(li)子，假(jia)如一(yi)個果(guo)(guo)園(yuan)目(mu)前的(de)有(you)機(ji)質含(han)量是1.0%（事實上(shang)，目(mu)前中國(guo)許多果(guo)(guo)園(yuan)的(de)有(you)機(ji)質含(han)量就只有(you)這(zhe)么(me)高），通過(guo)連(lian)年合理(li)負載，每年足量施入有(you)機(ji)肥(fei)，連(lian)年進行果(guo)(guo)園(yuan)生草，并(bing)將產的(de)草和(he)果(guo)(guo)樹落葉(xie)還田，這(zhe)樣的(de)話，每年這(zhe)個果(guo)(guo)園(yuan)的(de)有(you)機(ji)質含(han)量可(ke)以增(zeng)加0.1%，而要達(da)到6.8%，則需(xu)要50多年。

此(ci)外(wai)，與歐美等國(guo)家相(xiang)比，日(ri)(ri)本有(you)(you)(you)機(ji)(ji)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)業(ye)(ye)經營以(yi)小規模(mo)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)場和農(nong)(nong)(nong)(nong)(nong)(nong)(nong)戶占多數(shu)，有(you)(you)(you)機(ji)(ji)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)業(ye)(ye)主要以(yi)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)作物(wu)栽(zai)培(pei)為(wei)主，有(you)(you)(you)機(ji)(ji)畜(chu)牧業(ye)(ye)發展相(xiang)對比較(jiao)薄弱(ruo)。在實行(xing)有(you)(you)(you)機(ji)(ji)栽(zai)培(pei)的作物(wu)中，有(you)(you)(you)機(ji)(ji)稻米占50%，有(you)(you)(you)機(ji)(ji)蔬菜占35%等。除有(you)(you)(you)機(ji)(ji)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)產(chan)品(pin)外(wai)，日(ri)(ri)本還有(you)(you)(you)各類特別栽(zai)培(pei)的農(nong)(nong)(nong)(nong)(nong)(nong)(nong)產(chan)品(pin)，如無農(nong)(nong)(nong)(nong)(nong)(nong)(nong)藥(yao)、減(jian)化肥(fei)(fei)(fei)栽(zai)培(pei)的農(nong)(nong)(nong)(nong)(nong)(nong)(nong)產(chan)品(pin)，減(jian)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)藥(yao)、無化肥(fei)(fei)(fei)栽(zai)培(pei)的農(nong)(nong)(nong)(nong)(nong)(nong)(nong)產(chan)品(pin)，減(jian)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)藥(yao)、減(jian)化肥(fei)(fei)(fei)栽(zai)培(pei)的農(nong)(nong)(nong)(nong)(nong)(nong)(nong)產(chan)品(pin)等等。其栽(zai)培(pei)面(mian)積是有(you)(you)(you)機(ji)(ji)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)產(chan)品(pin)栽(zai)培(pei)面(mian)積的3~4倍。日(ri)(ri)本有(you)(you)(you)機(ji)(ji)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)業(ye)(ye)比較(jiao)注重(zhong)精耕(geng)細作，強調(diao)有(you)(you)(you)機(ji)(ji)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)業(ye)(ye)的功能和提(ti)(ti)高農(nong)(nong)(nong)(nong)(nong)(nong)(nong)產(chan)品(pin)的自給率，提(ti)(ti)倡減(jian)農(nong)(nong)(nong)(nong)(nong)(nong)(nong)藥(yao)、減(jian)化肥(fei)(fei)(fei)的生產(chan)方式。