To explore the effect of fertilization on the water quality of juvenile crab culture ponds, a field experiment was carried out in Chongming, Shanghai from June to October, 2016. Two groups with three replications each were set:(1) unfertilized group and (2) fertilized group. Water temperature(T), dissolved oxygen (DO), pH, chemical oxygen demand(COD_Mn), total phosphorus (TP), phosphate(PO₄^3--P), total nitrogen (TN), nitrate (NO₃^--N), nitrite (NO₂^--N), ammonia nitrogen (NH₄⁺-N), total hardness and chlorophyll a(Chl. a) of headwaters were monitored seasonally. The result indicated that water quality in the ponds had significant seasonal variation. The water quality factors were comparatively steady in June and September. COD_Mn and Chl. a increased significantly in July and August, while the DO decreased markedly. In the end of crab cultivation, most of the water quality factors increased significantly in two groups, but the total hardness and DO decreased greatly. There was no significant difference in T and pH between headwater and pond water (P > 0.05). DO and NO₃^--N of headwater were higher than ponds(P < 0.05). TP,PO₄^3--P, Chl. a and total hardness in unfertilized ponds were lower than fertilized ponds(P < 0.05). The juvenile crab ponds after fertilizing would cause temporary increase of of TN,NH₄⁺-N,NO₂^--N,NO₃^--N and COD_Mn. The study found that the difference of comprehensive benefits of two groups is not obvious. The fertilized group increased the N and P accumulation in pond and then aggravated the water pollution, having no more benefits than unfertilized group. Therefore, non-fertilization is more suitable for ecological cultivation.