Environmental stress, such as intense rainfall, drought and salinization, is predicted to increase not only in intensity, but also in frequency under future climate scenarios. Quantitative information about the response of the early recruitment process to environmental stress is essential for predicting the species distribution pattern; however, it is still lacking. We conducted an experiment in the rainproof shelter to investigate the response of early recruitment processes of Zizania latifolia at flooding depths of 0, 5, 15 and 30 cm and salinity of 0, 5, 15, 30 and 50 mmol/L. The effects of flooding depth and salinity on rhizome bud sprouting, shoot survival, and shoot early growth of Z. latifolia were investigated. The results showed that the interaction between flooding depth and salinity had no significant effect on the rhizome bud sprouting and obviously affected the shoot early growth. Flooding reduced final sprouting percentage and shoot survival, but enhanced the half-final sprouting time, absolute growth rate and shoot height. Salinity has no effect on final sprouting percentage and shoot survival. Both absolute growth rate and shoot height showed a unimodal relationship with salinity, while the half-final sprouting time showed a u-shaped pattern along the salinity gradient. We therefore conclude that Z. latifolia may be used for vegetation restoration of mild salinized wetlands (salinity less than 15 mmol/L), and artificially reducing the flooding depth (below 15 cm) during the establishment stage will be more conducive to the expansion of the Z. latifolia in the salt marsh.