In this paper, the Nanliuj river basin of Beibu Gulf, which flows into the Haihe River alone, was taken as the research object. Based on the land use data interpreted by remote sensing data in 2000 and 2015, and social and economic data, the CLUE-S model was applied to the ecological protection scenario in 2030. The land use patterns of natural growth scenarios and food security scenarios were simulated and predicted. On this basis, the InVEST model was used to evaluate the biodiversity of different scenarios in the past and future, and the habitat quality and degradation degree of biodiversity in the watershed were discussed. The results indicated:(1) From 2000 to 2015, the construction land, garden land, water area and unused land in Nanliu river basin showed an increasing trend, in which the construction land increased the most, while the cultivated land and woodland decreased the most. (2) There were 34 kinds of land network transfer flow relationships in the basin land system, including 24 in the upstream, 20 in the middle and 28 in the downstream. The conversion between cultivated land and construction land, cultivated land and forest land and between forest land and garden land accounted for 70.74% of the total land use change in the river basin. (3) When CLUE-S model was used to simulate future land use, Kappa coefficient reached 0.86, indicating that the land use accuracy of the model to simulate future scenarios met the requirements. (4) The total and average scores of habitat quality in the watershed of the 2000, 2015 and 2030 ecological protection scenarios, 2030 natural growth scenarios and 2030 food security scenarios were respectively 866630, 900357, 921055, 876231, 865370 and 0.7457, 0.7747, 0.7925, 0.7539 and 0.7466. (5) In the future 2030, the biodiversity of the three scenarios in the middle and upper reaches of the region and the lower reaches of the region showed different degrees of improvement, while the middle reaches showed degradation.