Abstract: Extreme weather events occur frequently in the desert region of northwest China, such as drought, high temperature, and strong radiation. Desert vegetation is often exposed to multiple environmental stresses. Plants in deserts are at risk of rapid degradation, particularly that those are sensitive to climate change. Therefore, it is necessary to explore the response of vegetation to environmental fluctuations in this region, aiming to clarify the regulatory mechanisms of desert plants to the environments, and thereby predict the succession and development of desert ecosystem communities under future climate change. Chlorophyll fluorescence technology can rapidly collect detailed information of photosystem II (PSII) energy distribution without damage, which is widely used for in situ monitoring environmental stress in plants. However, there are some lags of covariance between chlorophyll fluorescence parameters and related environmental factors by just visually examining their time series, particularly on timescales. Wavelet analysis can be selected to analyze transient dynamics between two-time series, providing valuable insights into the temporal dynamics of ecological time series and their environmental controls. Unfortunately, few studies were applied wavelet techniques to chlorophyll fluorescence measurements in desert ecosystems. In this study, an in-situ field measurement of chlorophyll fluorescence was conducted for Artemisia ordosica in the Mu Us desert, and then the Continuous Wavelet Transform (CWT) and Wavelet Coherence (WTC) analysis were selected to investigate how the Photosynthetically Active Radiation (PAR), air temperature, Vapor Pressure difference (VPD), and Soil Water Content (SWC) modulated the variability of PSII energy partitioning in the time-frequency domain. The results showed that: The CWT revealed that there were clear daily periodicities on the PSII energy partitioning parameters, such as the photochemical efficiency, regulated heat dissipation, and non-regulated heat dissipation, indicating a strong oscillation at intermediate scales (days to weeks). On the diurnal scale, the continuous areas of significant WTC were observed between PSII energy partitioning parameters and environmental factors during growing seasons, 43 min, 3.3, 4.6 and 10.72 h lagged behind PAR, air temperature, VPD and SWC, respectively (P<0.05). This can imply that the heat dissipation in the lutein cycle and the change of stomatal conductance can be the underlying mechanisms regulating the energy partitioning of PSII on a short timescale. On the seasonal scale, non-continuous areas of significant WTC were observed between PSII energy partitioning parameters and environmental factors, 7.2, 8.8, 14.7, and 21.6 days lagged behind air temperature, VPD, PAR, and SWC, respectively (P<0.05). It infers that the repairing capacity of PSII, the amount of specific protein, and chlorophyll concentration can be the underlying mechanisms regulating the energy partitioning of PSII on a long timescale. The fluctuations of the maximal quantum yield of PSII photochemistry and PSII energy partitioning parameters of Artemisia ordosica were basically consistent with the vegetation phenological period. In July and August, maximal quantum yield of PSII photochemistry and ΦPSII decreased, whereas, regulated heat dissipation and non-regulated heat dissipation increased. In May and September, non-regulated heat dissipation increased, while maximal quantum yield of PSII photochemistry decreased. This demonstrated that the mechanisms of Artemisia ordosica regulating PSII energy partitioning depended mainly on different time scales. It was also found that Artemisia ordosica can repair the damaged PSII by itself in the harsh environment, especially in a desert, returning to normal physiological level in which the maximal quantum yield of PSII photochemistry remained around 0.78, indicating that a strong tolerance to drought and high radiation. This study can provide a scientific reference to real-time monitor the crop growth, and thereby protect the agricultural ecology system in the desert.