Taking Min River delta as an example, in order to explore the scientificity of different evaluation methods for landscape connectivity, a cost distance index based on the minimum cost distance model was proposed to characterize landscape functional connectivity, and compared with the traditional landscape structure connectivity index based on landscape pattern index. The aim is to reveal the spatial coupling relationship between the two, and provide support for effective evaluation of landscape connectivity. The results showed that:(1) From 2000 to 2020, the conversion of forest land to construction land was 370.72 km², accounting for 77.28% of the total conversion area. The conversion of grassland and cultivated land into forest land was 80.45 km², accounting for 90.53% of the total conversion area. (2) During the past 20 years, the structure and functional connectivity of forest land showed a decreasing trend in general. Among which, the decrease of the structure and functional connectivity of forest land in Huli area was the largest, and the patch density, the largest patch index, aggregation index and patch cohesion index decreased by 76.47%, 51.33%, 68.13%, and 68.40%, respectively. The cost distance index increased by 178.56%. (3) The cost distance index was negatively correlated with patch density, the largest patch index, aggregation index, patch cohesion index, and integrated index of landscape structure connectivity. (4) During the study period, the bivariate local spatial autocorrelation aggregation type changed from low-high to high-high, and the landscape functional connectivity decreased when the structural connectivity did not change. From high-high to low-high, the landscape functional connectivity increased when the structural connectivity did not change. The results showed that the cost distance index was more sensitive to landscape functional connectivity than the landscape structure connectivity index. Therefore, cost distance index has advantages in measuring landscape connectivity in rapidly urbanized areas. However, the applicability of landscape pattern index and cost distance index is similar in areas with higher elevation, complex terrain and less human disturbance. The research results can provide a scientific reference for biodiversity conservation in Min River Delta, and provide a new way to study the impact of different methods on landscape connectivity evaluation.