China’s southwestern special terrain pattern as parallel arrangement between longitudinal towering mountains and deep valleys has significant effects on the differentiation of local natural environment and eco-geographical pattern in this region. The 1:50,000 Digital Elevation Model (DEM) data of Longitudinal Range-Gorge Region (LRGR), meteorological observation data from the station establishment to 2010, hydrological observation data, Normalized Difference Vegetation Index (NDVI) and Net Primary Productivity (NPP) products of MOD13 and MOD17 as well as 1:1,000,000 vegetation type data were used. Moisture indices including surface atmospheric vapor content, precipitation, aridity/humidity index, surface runoff, and temperature indices including average temperature, annual accumulated temperature, total solar radiation were selected. Based on ANUSPLIN spline function, GIS spatial analysis, wavelet analysis and landscape pattern analysis, regional differentiation characteristics and main-control factors of hydrothermal pattern, ecosystem structure and function in this region were analyzed to reveal the effects of terrain pattern on regional differentiation of eco-geographical elements. The results show that: influenced by terrain pattern, moisture, temperature and heat in LRGR have shown significant distribution characteristics as intermittent weft differences and continuous warp extension. Longitudinal mountains and valleys not only have a north-south corridor function and diffusion effect on the transfer of major surface materials and energy, but also have east-west barrier function and blocking effect. Special topographic pattern has important influences on vegetation landscape diversity and spatial pattern of ecosystem structure and function, which is the main-control factor on vegetation landscape diversity and spatial distribution of ecosystem. Wavelet variance analysis reflects the spatial anisotropy of environmental factors, NDVI and NPP, while wavelet consistency analysis reveals the control factors on spatial distribution of NDVI and NPP as well as the quantitative relationship with control degree. Special terrain pattern in LRGR is the major influencing factor on eco-geographical regional differentiation in this region. Under the combined effect of zonality and non-zonality laws with “corridor-barrier” function as the main characteristic, special spatial characteristics of eco-geographical regional system in LRGR is formed.