From 2014 to 2015, we investigated and compared the Hami and Wuqia populations of Gymnocarpos przewalskii in the wild, and used indices such as flowering amplitude, relative flowering intensity, synchrony index. The two populations flowered once in a year, late April to early May into flowering onset; the flowering phenology of the two populations was similar, and the plant has the characteristics of high flowering synchrony and a typical “mass flowering” pattern. At the individual level, there were significant differences both in the first flowering date and the end flowering date by population and year; the single flower longevity and mean longevities of individual flowers were similar at different years. Different populations differed: the flowering duration of a single flower of Wuqia was slightly longer than for the Hami population. We found a significant positive correlation between flower number and seed number, whereas the synchrony indices were negatively correlated with relative flowering intensity in different populations. The similarity in flowering amplitude and flowering synchrony in the two species and years of G. przewalskii may be explained by their phylogenetic relationships, whereas the differences may result from their evolutionary history in heterogeneous habitats (altitude, temperature, precipitation and light). These results can provide useful information for research on reproductive biology and conservation for the species.