Soil organic matter (SOM) is a key index of soil fertility. Calculating spectral index and screening characteristic band reduce redundancy information of hyperspectral data, and improve the accuracy of SOM prediction. This study aimed to compare the improvement of model accuracy by spectral index and characteristic band. This study collected 178 samples of topsoil (0–20 cm) in the central plain of Jiangsu, East China. Firstly, visible and near-infrared (VNIR, 350–2500 nm) reflectance spectra were measured using ASD FieldSpec 4 Std-Res spectral radiometer in the laboratory, and inverse-log reflectance (LR), continuum removal (CR), first-order derivative reflectance (FDR) were applied to transform the original reflectance (R). Secondly, optimal spectral indexes (including deviation of arch, difference index, ratio index, and normalized difference index) were calculated from each type of VNIR spectra. Characteristic bands were selected from each type of spectra by the competitive adaptive reweighted sampling (CARS) algorithm, respectively. Thirdly, SOM prediction models were established based on random forest (RF), support vector regression (SVR), deep neural networks (DNN) and partial least squares regression (PLSR) methods using optimal spectral indexes, denoted here as SI-based models. Meanwhile, SOM prediction models were established using characteristic wavelengths, denoted here as CARS-based models. Finally, this research compared and assessed accuracy of SI-based models and CARS-based models, and selected optimal model. Results showed: (1) The correlation between optimal spectral indexes and SOM was enhanced, with absolute value of correlation coefficient between 0.66 and 0.83. The SI-based models predicted SOM content accurately, with the coefficient of determination (R2) and root mean square error (RMSE) values ranging from 0.80 to 0.87, 2.40 g/kg to 2.88 g/kg in validation sets, and relative percent deviation (RPD) value between 2.14 and 2.52. (2) The accuracy of CARS-based models differed with models and spectral transformations. For all spectral transformations, PLSR and SVR combined with CARS displayed the best prediction (R2andRMSEvalues ranged from 0.87 to 0.92, 1.91 g/kg to 2.56 g/kg in validation sets, andRPDvalue ranged from 2.41 to 3.23). For FDR and CR spectra, DNN and RF models achieved more accuracy (R2andRMSEvalues ranged from 0.69 to 0.91, 1.90 g/kg to 3.57 g/kg in validation sets, andRPDvalue ranged from 1.73 to 3.25) than LR and R spectra (R2andRMSEvalues from 0.20 to 0.35, 5.08 g/kg to 6.44 g/kg in validation sets, andRPDvalue ranged from 0.96 to 1.21). (3) Overall, the accuracy of SI-based models was slightly lower than that of CARS-based models. But spectral index had a good adaptability to the models, and each SI-based model displayed the similar accuracy. For different spectra, the accuracy of CARS-based model differed from modeling methods. (4) The optimal CARS-based model was model CARS-CR-SVR (R2andRMSE: 0.92 and 1.91 g/kg in validation set,RPD: 3.23). The optimal SI-based model was model SI3-SVR (R2andRMSE: 0.87 and 2.40 g/kg in validation set,RPD: 2.57) and model SI-SVR (R2andRMSE: 0.84 and 2.63 g/kg in validation set,RPD: 2.35).