Influence of the agricultural management practices on soil quality and the ecosystem functions has been an increasing concern in soil science and ecology with sustainable agriculture. This study deals with the soil earthworm community changes under different fertilization schemes in a paddy soil under long-term different fertilizations. The studied soil is located in Wujiang Municipality, Jiangsu Province, China and had been cultivated under rice-rape rotation since 1987. The treatments are as follows: no fertilizer application (NF); chemical fertilizer only (CF); chemical fertilizer plus rice straw return (CSF) and chemical fertilizer plus pig manure (CMF). The amount of chemical fertilizer per year is N as urea 28.5 kg/hm^２, P₂O₅ as super phosphate 3.0kg/hm^２, KCl 5.6 kg/hm^２ and that of rice straw return is 300 kg FW/hm^２ and of manure 1120 kg FW/hm^２ respectively. The soil earthworms were collected and counted in the field from different fertilizer treated plots after rape harvest in May 2004, and their taxonomic groups examed under binocular stereoscope at laboratory. The earthworm body was crashed and protein separated by cell crasher, and the protein molecules with different sizes were analyzed by electrophoresis. Furthermore, another portion of earthworms collected was hydrolyzed and the aliquots were subjected to amino acid auto-analyzer. The results showed that totally 7 species of earthworms were recognized in the paddy filed with the number varying with different fertilization treatments. The earthworm community structure was much affected by the fertilization practice. Under chemical fertilization only, both number of earthworm species and quantity of individuals were significantly smaller than under the other treatments. Furthermore, there was an obvious decrease in the total amino acid and contents of most amino acids of the earthworms under chemical fertilization only compared to of those under combined fertilization of chemical and organic fertilizers. Whereas, chemical fertilizers in combination with rice straw return increased earthworm amino acid content, while long term pig manure application tended to increase earthworm protein content. As a molecular footprint, long-term chemical fertilization caused reduction of the content of protein with MW less than 25 kd but significant increase in that of protein with molecule size around 33 kd. This study demonstrated that different fertilization affect not only earthworm population but also diversity and richness in the paddy soil after 16 years of treatment and that long term chemical fertilization only may impact soil fauna community and thus, influence the paddy ecosystem functioning as of yield stability. This study implicated also that not only the community structure but also the amino acid metabolism as life functioning of earthworm in cropland soils may pose significant responses to the agricultural management practices.