It is a common responsibility of all countries to protect the ecological environment and promote sustainable development. Eco-geology, which provides a basic guarantee for the rational utilization of natural resources, ecological protection and restoration, has gradually become a new hot spot of geological survey institutions in various countries. Eco-geological survey in the Qinghai–Tibet Plateau plays an important role in regional ecological protection and global change research. Setting up workable budgets symbolizes the competence of geological survey organizations in fulfilling their responsibilities, and unreliable cost estimates can cause economic and political complications. The unclear scope definition and scarcity of project information available at early stages make it hard to generate reliable preliminary cost estimates. Hence, based on historical data and the practical experience of scientists who have been engaged in eco-geological survey in the Qinghai–Tibet Plateau for a long time, this research aimed to develop a cost estimation model using statistical learning methods for geological survey organizations to forecast preliminary costs during the early stages of an eco-geological survey project to fulfill different cost control and managerial functions. This research makes full use of modern remote sensing technology and reasonably arranges the input of ground survey, drilling, geophysical exploration and other workloads, supplemented by the existing ecological monitoring station data. It comprehensively sorts out the work means and workload of field and office work needed to complete the map work, and it puts forward a consistent index system and preliminary cost calculation framework. On this basis, based on the principle of matching quantity and price, a reasonable budget standard or market price is selected to calculate the budget estimate of a single map sheet, and then, through the regional adjustment coefficient, the budget estimate of a map sheet covering the whole Qinghai–Tibet Plateau is extended and calculated. The budget estimate will provide effective support for the declaration of eco-geological survey projects in the Qinghai–Tibet Plateau and the calculation of the scale of project funds so as to ensure the smooth development of eco-geological surveying in the region.