[en] Cascading stages of high-gain harmonic generation (HGHG) have been demonstrated to be a promising candidate for producing fully coherent soft X-ray radiation directly from UV seed sources. However, the large shot-to-shot output pulse energy fluctuation may still be a serious problem for its user applications. In this paper, we study the effects of various electron beam parameters jitters on the output pulse energy fluctuations of a two-stage HGHG. Theoretical calculations and intensive simulations have been performed and the results demonstrate that the relative timing jitter between the electron bunch and the seed laser pulse is mainly responsible for the large output pulse energy fluctuation. Several methods that may be helpful to improve the FEL stability have also been discussed.