With a municipal and county-level agricultural geological survey in a typical eastern region of Hainan Province as a case study, the MapGIS-based Label point method is introduced for sample point layout. The lands involved in the second land use survey of Hainan Province are incorporated into 10 categories comprising dry land, paddy field, orchards, other gardens, woodland, construction land, mudflat, traffic area, water surface and other land, and the number of pattern spots is reduced from 9,932 to 4,257 after the incorporation; then, the incorporated pattern spots are divided into three levels of A, B and C with descending representativeness in accordance with their area sizes; during the layout design of sample points, the traditional 500 m × 500 m grid method is adopted for Level-A pattern spots, the MapGIS-based Label point method for Level-B pattern spots, but no sample point layout design for Level-C pattern spots. After an automatic arrangement of sample points is carried out by software and necessary manual adjustment is conducted, a total of 1,610 sampling points are arranged in the working region covering an area of 174 km², and the density of the sample point reaches 9.25 point/km², which meets the relevant requirements of the agricultural geological survey. The validation test of the method suggests that, compared with the traditional 333 m×333 m grid method of sample point layout, the method proposed in this paper has significant superiority in workability, representativeness, accuracy and reasonableness and hence deserves extensive promotion and application.