Based on land use data from three periods, land use/cover change and ecological services values (ESV) in Shenzhen were analyzed based on the value equivalent factor in a unit area. In addition, the effects of the basic ecological control line policy on the ESV in Shenzhen were investigated using the difference in differences method. The results indicated that the quantities of cultivated land, orchard, grassland, and water bodies decreased from 2002 to 2010, whereas construction land area increased. In addition, the forest land first increased then decreased, but the decrease ratio showed a reduction trend after the basic ecological service control line policy was implemented. Among all land use types, forest land and water bodies were the two main sources of ESV, whereas water supply had the top value among all kinds of services. Areas with low ESV expanded and eroded the areas with high ESV. ESV on the western coast, the northern part of Bao'an and Longhua Districts, Guangming District, and the southern part of Longgang District decreased sharply. The grades of ESV within the control line zones were mainly medium and relatively high, while ESV outside the control line were mainly low and relatively low, which showed a decrease tendency. The results of the difference in differences method indicated that the basic ecological control line policy can increase ESV by approximately 1.6%.