The rapid and accurate diagnosis of nitrogen content in apple orchard soil is of great significance for the rational application of nitrogen fertilizer in orchards to improve apple yield and quality. An apple orchard in Shuangquan Town, Changqing District, Jinan City, Shandong Province, was taken as the experimental area. The optimal method for extracting spectral characteristic bands and screening spectral characteristic indices (SCIs) of soil total nitrogen (TN) for independent and comprehensive fertilization periods was explored. Independent and comprehensive soil TN content estimation models were constructed and optimized for each and the entire fertilization period, respectively. The results show that compared with the correlation coefficient method, stepwise multiple linear regression (SMLR) performs better in extracting hyperspectral characteristic bands of soil TN content. It helps to achieve a higher modeling accuracy, smaller root mean square error (RMSE), and is more conducive to avoiding the influence of multicollinearity of model variables. The sensitive areas of soil TN content in the SCI do not undergo significant changes due to different fertilization periods. Among them, the ratio spectral indices (RSIs) are in the range of 800–900 nm, 1900–1950 nm, and 2200–2300 nm, while the sensitive areas of the difference spectral index (DI) and Normalized difference spectral index (NDSI) are in the range of 1900–1950 nm and 2200–2300 nm. The combination of SCI and characteristic bands significantly improves the prediction accuracy of soil TN estimation models. The independent and comprehensive estimation models for each fertilization period based on the BP (back propagation) neural network optimized by the Mind Evolution Algorithm (MEA-BPNN) can achieve a more stable and accurate estimation of soil TN. Finally, using soil spectral characteristic bands selected through continuum removal (CR) transformation and SMLR, combined with SCI, the model based on the MEA-BPNN (CR-SCI-MEA-BPNN) has the best prediction performance. The modeling determination coefficients R2 for each fertilization period reached 0.94, 0.95, 0.92, and 0.94, respectively, with RMSE of 0.0032, 0.0024, 0.0035, and 0.0027. The R2 and RMSE of the modeling and validation set of the entire fertilization period comprehensive model are 0.899, 0.0038, and 0.89, 0.0041, respectively. The results of this article provide technical support for promoting the timely monitoring of soil TN content and guiding rational fertilization in apple orchards.