Under the rape-rice-rice cropping system, soil intensification is high, meanwhile, the higher crop yields could require higher soil fertility. Therefore, finding reasonable organic fertilizations is of significant importance in guiding the improvement of crop yields under the triple cropping system. In the field experiment, three fertilizations were applied, namely, (1) without organic materials as control (CK), (2) application of pig manure treatment (PM) and (3) application of biochar treatment (BC). The crop yield, soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), soil dissolved organic carbon (SDOC) and soil dissolved organic nitrogen (SDON) were measured from 2018 to 2019, and the correlation between crop yield and soil carbon and nitrogen indicators was analyzed. The results showed that: both PM and BC treatments significantly increased crop yield. Compared with CK, the total grain yield of three seasons in 2018 and 2019 under PM and BC treatments was increased by 8.9% - 13.8% and 10.3% - 15.1%, respectively. Notably, the grain yield of three seasons in BC treatment was significantly higher than that in PM treatment. At the same time, the contents of SMBC, SMBN, SDOC and SDON in PM and BC treatments were significantly higher than those in CK. However, there was no significant difference between BC and PM treatments. The parameters of fitted equation indicated that the correlation coefficient between soil microbial biomass nitrogen and the total grain yield of three seasons was higher than others. Thus, in the triple cropping system, both applications of pig manure and biochar can increase crop yield, and improve soil carbon and nitrogen contents. Furthermore, soil microbial biomass nitrogen is a key indicator for improving crop yield.