Net ecosystem productivity (NEP) is important in the carbon cycle. However, the divergent responses of NEP to climate change along topographical gradient, particularly slope, and aspect, is not yet well understood. This study investigates divergent response of NEP to climate change during 1981–2018 along topographical gradient by Ensemble Empirical Mode Decomposition and multiple regression. The results indicate that: (a) NEP increases at low elevations, but first decreases and then increases at mid‐high elevations, and decreases at high elevations. NEP increases with slope. NEP is higher in the east and west but lower in the north and south. (b) With elevation increasing, negative correlation of temperature (TEM) and vapor pressure deficit (VPD), along with the positive correlation of precipitation (PRE) and Solar radiation (SR) strengthens first and then weaken, but PRE's positive correlation strengthens again after 4,000 m, and TEM's negative correlation changes to positive at high elevations. Moreover, soil moisture (SM's) positive correlation strengthens overall. NEP changes are dominated by PRE and VPD below 2,000 m, by TEM and PRE at 2,000–4,000 m, and by PRE and SM above 4,000 m. (c) With slope increasing, the negative correlation of TEM and the positive correlation of SM and SR and their importance strengthen. While PRE's positive correlation and VPD's negative correlation, and their importance weaken. (d) NEP changes are controlled by PRE and VPD in all respect, but the positive relationship of PRE and its importance weakens from north to west, opposite to VPD. Our results highlight the importance of topography for deeply understanding NEP's response to climate changes.