Global ocean heat content (OHC) is generally estimated using gridded, model and reanalysis data; its change is crucial to understanding climate anomalies and ocean warming phenomena. However, Argo gridded data have short temporal coverage (from 2005 to the present), inhibiting understanding of long-term OHC variabilities at decadal to multidecadal scales. In this study, we utilized multisource remote sensing and Argo gridded data based on the long short-term memory (LSTM) neural network method, which considers long temporal dependence to reconstruct a new long time-series OHC dataset (1993–2020) and fill the pre-Argo data gaps. Moreover, we adopted a new machine learning method, i.e., the Light Gradient Boosting Machine (LightGBM), and applied the well-known Random Forests (RFs) method for comparison. The model performance was measured using determination coefficients (R2) and root-mean-square error (RMSE). The results showed that LSTM can effectively improve the OHC prediction accuracy compared with the LightGBM and RFs methods, especially in long-term and deep-sea predictions. The LSTM-estimated result also outperformed the Ocean Projection and Extension neural Network (OPEN) dataset, with an R2 of 0.9590 and an RMSE of 4.45 × 1019 in general in the upper 2000 m for 28 years (1993–2020). The new reconstructed dataset (named OPEN-LSTM) correlated reasonably well with other validated products, showing consistency with similar time-series trends and spatial patterns. The spatiotemporal error distribution between the OPEN-LSTM and IAP datasets was smaller on the global scale, especially in the Atlantic, Southern and Pacific Oceans. The relative error for OPEN-LSTM was the smallest for all ocean basins compared with Argo gridded data. The average global warming trends are 3.26 × 108 J/m2/decade for the pre-Argo (1993–2004) period and 2.67 × 108 J/m2/decade for the time-series (1993–2020) period. This study demonstrates the advantages of LSTM in the time-series reconstruction of OHC, and provides a new dataset for a deeper understanding of ocean and climate events.