How to address soil carbon (C) sequestration and crop straw recycling is an intractable challenge for agriculture. The application of various agricultural straws (including fresh straw, decomposed straw, straw-derived biochar) to soil alters the soil C pool. In order to understand soil C dynamics and the potential C sequestration characters after the addition of straw and/or straw-derived biochar, an in-situ mesocosm experiment was conducted under five treatments as (1) no straw and no biochar control (CT), (2) straw addition only (ST), (3) straw with a straw-decay bacterium (STDB), (4) biochar addition only (BC) and (5) a combination of straw with biochar (STBC). Carbon dioxide (CO2) flux from soil, total soil organic C (SOC) and soil labile organic C (LOC), as well as soil aggregate associated organic C have been analyzed within a dryland rape-maize cropping system. The results showed that soil CO2 flux increased with the addition of crop straws (ST, STBC and STDB), but decreased under BC because of a lower LOC under BC, especially microbial biomass C fraction in the LOC. The combined application of STDB increased the percentages of macro-aggregates (>2 mm and 0.25–2 mm). Meanwhile, the decomposition of organic matter was increased, and the CO2 flux was also increased. The 0.053-0.25 mm aggregate under BC had the highest fine intra-aggregate particulate organic C (iPOC), which promoted C sequestration. However, the higher coarse-iPOC in >2 mm and 0.25–2 mm aggregates under ST and STDB promoted SOC decomposition and also CO2 flux. Compared with all three straw treatments (ST, STBC and STDB), the sole biochar addition reduced CO2 flux while increased net C sequestration without significant decreases of crop yields and net primary productivity. The sole biochar addition did improve the physical protections for SOC from soil aggregates. The obtained results showed differential responses of soil C pool and aggregates associated organic C to straw and/or straw-derived biochar addition while providing insights into potential soil C sequestrations or mitigations by using agriculture based organic materials.