The timing of flowering phenology in most temperate trees results from the interplay of winter chilling and spring heat. As global warming progresses, reduced chilling may gain increasing importance in regulating flowering dates, and eventually offset flowering advances in response to warmer springs. Later onset of flowering events may arise, with negative effects on plant fitness. However, delayed flowering in trees may also reduce the risk from late frosts. Different temperature conditions at both margins of the apple growing areas of Shaanxi in China provide a natural laboratory to examine the responses of trees’ flowering phenology and late frost risk to climate warming. We identified the chilling and heat accumulation periods for apples by Partial Least Squares regression of first flowering dates against daily chilling and heat accumulation rates during 2001–2016. We then analyzed the impacts of temperatures during these periods on flowering timing, and evaluated the frost risk for each site. Results indicated increasing importance of chilling temperatures from north to south, with greatest effects determined for the warmest site, where delayed blossom has been observed during the past 16 years. Since late frosts mostly occurred before tree flowering, only minor frost damage was detected for our study areas, with future delays in flowering likely to reduce the frost risk even further. The redistribution of apple trees to nearby locations with cold winters, either northward or uphill, could be a promising strategy to reduce the risk of insufficient chilling and ensure that production remains viable in a warming future.