Under the background of global climate change, the intensity and frequency of precipitation will change in the future, and extreme precipitation events can significantly increase the ammonium content in water column in a short period of time, which will affect the growth of submerged macrophytes. However, the physiological and morphological response of submerged macrophytes to different ammonium pulse pattern (i.e., concentration and frequency) is still unclear. Two common submerged macrophytes (i.e., Vallisneria natans and Hydrilla verticillata) were selected, and different substrates (i.e., clay and sand), ammonium pulse patterns (i.e., CK: control, no ammonium addition; P1: low concentration×high frequency; P2: high concentration×low frequency) and experimental phases (ammonium pulse phase and release pulse phase) were set up to assess the effects of different pulse patterns on plant traits and potential effects after pulse release by measuring plant morphological and physiological traits. The results showed that: (1) Ammonium pulse changed the morphological and physiological traits of submerged macrophytes, with ammonium pulse pattern of high concentration and low frequency having the greatest inhibitory effect on plant growth compare to the pattern of low concentration and high frequency. (2) One month after the release of ammonium pulse, plant biomass of the two species had no difference compared to the control, while the physiological traits (e.g., free amino acid and soluble carbohydrate) showed significant differences compared with the control. These results indicated that the morphological traits were mostly recovered from ammonium pulse, while the effects on the physiological traits of the submerged macrophytes were still intense and time-lasting. (3) In the phase of releasing pulse, the free amino acid content of V. natans was still significantly higher than that of the control, while the free amino acid content of H. verticillata was less different from that of the control, indicating that the assimilation and turnover efficiency of ammonium was higher in H. verticillata than V. natans. (4) The substrate type affected the response of physiological traits to ammonium pulse, that is, the change of free amino acid and soluble carbohydrate contents in sand was larger than that in clay. Therefore, the ammonium pulse effects were closely related to the pulse concentration and frequency, substrate type, plant species and their morphological and physiological traits. Our findings highlight the importance of plant physiological traits in assessment of plant environmental adaptability, and provide scientific reference for the management of submerged macrophytes in lake ecosystems under global climate change.