Long nanosecond pulses have been proven to be efficient at enhancing underwater LIBS emission. However, the quantitative analytical capability of underwater long-pulse LIBS has yet to be further revealed. In this work, we investigated the spectral characteristics by irradiating with a laser pulse of 120 ns duration. The alkali and alkaline earth metals Li, K and Ca and the transition element Mn were selected for analysis. It is shown that obvious self-reversal structures were observed in the spectra at high concentrations, making the calibration curves saturated. Correction was performed using the approximate Voigt function fitting method, which significantly improves the linearity of the calibration curves. In addition to the target metal elements, atomic lines of the matrix elements H and O in water were also observed, which can serve as promising internal standards for quantitative analysis. A comparison of the quantification performance with and without the internal standards demonstrates that the use of the internal standards is conducive to improving the robustness of the calibration approaches with higher determination coefficients. More importantly, the underwater LIBS signal stability is improved by more than 3 times, and the prediction error for validation samples is reduced by 2–4 times. The present results suggest that long ns pulses are favorable to significantly improving the qualitative and quantitative performance of underwater single-pulse LIBS, enabling long-pulse LIBS to have great potential to be applied to underwater in situ chemical analysis.