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Carbon-nitrogen ratio (C/N) and carbon-sulphur ratio (C/S) of unknown samples can vary greatly in the natural environment. There are also distinct differences in the ionization efficiencies of N and S elements. These factors will introduce the fluctuation of signal intensity to the element analysis-isotope ratio mass spectrometry (EA-IRMS), which can has a further impact on the measurements of sample δ15N and δ34S. However, the analysis of unknown sample δ15N and δ34S is always restricted by the low content or the scarcity of the target elements. In this study, we focused on the effect of sample amount and signal intensity on the δ15N and δ34S measurement by EA-IRMS. Our results indicated that the EA-IRMS measurement of δ15N and δ34S was significantly affected by the “blank effect” when the sample amount and signal intensity were limited during the mass spectrometry analysis. Under the injection conditions of 1.71-561.93 μg N and 3.74-100.62 μg S, the variation ranges of the measurement errors of the isotopic reference materials δ15N and δ34S were 0.18‰-0.54‰ and 0.21‰-0.88‰, respectively. Meanwhile, the variation ranges of the measurement errors of measurement precision were 0.24‰-0.57‰ and 0.27‰-0.54‰, respectively. With the high C/N and C/S wood samples, the measurement errors of EA-IRMS were 0.34% for δ15N. Because the true value of the above wood sample δ34S was unknown, the measurement precision of EA-IRMS on the wood samples was 0.58‰. Based on the analysis of two wood sample δ15N, the EA-IRMS had a good time stability during the continuous (6-20 days) measurement process. We hoped these findings could provide implications for the application of EA-IRMS in biogeochemistry and life science areas.