Abstract: It is of great practical significance to study the causes and mechanism of fruit price fluctuations from the perspective of spatial economics. Taking apple and banana markets from 2000 to 2014 as examples, and applying the revised Gini coefficient and Moran’s Ⅰ index, this paper investigated the spatial distribution and variation characteristics of China’s fruit markets. This paper also empirically tested the influence of the spatial distribution on the price fluctuations of apple and banana markets by the X-12-ARIMA seasonal adjustment model and covariance analysis. Results show that: 1) China’s fruit production displays an obvious geographic concentration feature: fruit production and consumption regions are separated with huge inter-reginal trade flows. At the same time, fruit production concentration has been shifting from the east to the west. 2) Apple and banana price fluctuations of main production areas are more intense than that of main consumption areas. The intensity of fluctuations of apple and banana prices may be related to regional economic development levels. And 3) general trend change and seasonal change are the main sources of apple and banana price fluctuations, with the former having more contribution to apple and banana price fluctuations of main consumption areas. The irregular changes on apple and banana price fluctuations of main production areas are larger than that of main consumption areas.