The widespread utilization of straw return was a popular practice straw disposal for highly intensive agriculture in China, which has brought about some negative impacts such as less time for straw complete biodegradation, aggravation of greenhouse gas evolution, and lower efficient of carbon accumulation. It was urgent to find an eco-friendly N-rich organic fertilizer instead of mineral N as activator to solve the above problems and lead a carbon accumulation in long tern management. Besides, microbial necromass was considered as a crucial contributor to persistent soil carbon (C) and nitrogen (N) pool. How organic fertilizer activators influence microbial residue under different amount of crop residues input remained unclear. Thus, soils incorporating moderate and high rate of rice straw residue with additions of half and full of organic activators (fish protein hydrolysates vs. manure) were incubated for measuring carbon dioxide (CO2) and nitrous oxide (N2O) emission, microbial community and necromass. It was found that soil CO2 emission was rapidest during the first 13 days of straw decomposition but remained lowest in the treatments of 50% mineral N substituted by fish protein hydrolysate. There were that 81%–89% of total CO2 release and 59%–65% of total N2O emission occurred within 60 days of incubation period, and bacterial community and nitrate positively affected soil CO2 and N2O release respectively. Straw incorporation amount and organic activator application interactively influenced soil CO2 emission but not affected soil N2O emission. After 360 days of incubation, the difference of bacterial necromass was noticeable but fungal necromass remained almost unaltered across all treatments. All treatments showed generally comparable contribution of microbial necromass N to the total N pool. The treatment of 50% mineral N substituted by fish protein hydrolysate under high rate of straw input (HSF50) promoted the highest proportion of microbial necromass C in soil organic C because of alleviating N limitation for microorganisms. Finally, HSF50 was recommended as an eco-friendly strategy for enhancing microbial necromass C and N storage and climate benefits in agroecosystems.