Assessment of the conservation effectiveness of nature reserves (NRs) is an important basis for the management and optimization of NRs. National NRs (NNRs) and provincial NRs (PNRs) in Yunnan Province were chosen for this study and the normalized difference vegetation index (NDVI) was provided by SPOT_Vegetation. Based on the trend of NDVI change (the method of single linear trend) and the stability of NDVI change (the method of coefficient of variation), the study compared and analyzed the differences of plant production between internal and external NRs to evaluate the conservation effectiveness of the NRs. The results showed that: (1) the whole conservation effectiveness of NNRs and PNRs in Yunnan Province was good from 1998 to 2015. The NDVI of internal and external NRs increased significantly, and the proportion of the number of internal and external NRs with significant NDVI growth was 64.81% and 79.63% respectively. In terms of spatial distribution, NRs with significant NDVI growth were concentrated on the central, northeast and southeast of Yunnan Province. (2) There was no significant difference in the NDVI coefficient of variation between internal and external NRs in Yunnan Province. 51.85% of NRs had better conservation effectiveness because the internal vegetation growth was more stable than the external vegetation growth of these NRs. They were mainly distributed in the west, southwest, southeast and northeast of Yunnan Province. It failed to reflect the significant difference between the internal and external protection effectiveness of the NRs. (3) The protection effectiveness of NNRs was generally better than that of PNRs in Yunnan Province. (4) In terms of the type of NRs, the protection effectiveness of forest ecosystem NRs was good, while wild plant NRs and wild animal NRs had moderate conservation effectiveness, and the conservation effectiveness of wetland ecosystem NRs worsened in effectiveness. This research can provide a reference for exploring the assessment methods of conservation effectiveness of the protected areas network on the regional scale, and support the optimization and perfection of NRs in Yunnan Province.