Achieving carbon neutrality in the pulp and paper industry necessitates effectively recycling pulp and papermaking wastewater, where continuous monitoring of effluent quality indices is crucial. This study suggests a novel machine learning-based model named LSTMAE-XGBOOST that integrates the feature extraction capabilities of autoencoder, the sequential feature learning capabilities of LSTM, and the high prediction accuracy of XGBOOST. This model is capable of extracting the complex relationships, non-Gaussian characteristics, and time series features from the papermaking wastewater data, and it demonstrates superior predictive performance. Compared to traditional machine learning models, the proposed model exhibits higher prediction accuracy. Specifically, when contrasted with partial least squares regression, LSTMAE-XGBOOST achieves a 40% increase in R2 and a 35% reduction in RMSE. Further comparative assessments against other machine learning-based hybrid models with similar structures confirm the superiority of integrating LSTM and XGBOOST within the hybrid model approach. This study contributes a compelling methodology for modeling effluent quality indices, offering significant implications for environmental management in the pulp and paper industry.