The ecological footprint method was initially proposed by Rees in the early 1990s, and Wackernagel and Niccolucci subsequently developed this method into two-and three-dimensional models. Ecological footprint models, as tools to estimate the appropriation of natural resources by humans, are important to evaluate the land carrying capacity. Using the three-dimension model, this paper expanded the footprint depth value range from ≥ 1 to ≥ 0, and the ecological deficit and remainder were then analyzed. Using a modified three-dimensional model, the ecological footprint, footprint depth, and ecological deficit (remainder) in Wenzhou City were calculated from 2000 to 2012. On this basis, the food pressure, water pressure, carbon sink pressure, construction pressure, and land comprehensive load indexes were introduced to the indicator system of land carrying capacity, and the condition of load carrying of Wenzhou City was determined. The results showed that from 2006 to 2012, the ecological footprint per capita increased annually, and since the biologically productive land remained unchanged, the ecological deficit worsened and a greater load was imposed on the land in Wenzhou City. The footprint depth value ranged from 4 to 6, which meant that natural resource flows could not meet the demand of everyday residential consumption, and natural resource stocks were extensively depleted. The food pressure, water pressure, carbon sink pressure, and land comprehensive load indexes were > 1, which indicated that arable land, sea, and forest were overloaded. Since 2000, the load, primarily from food and carbon sink pressures, imposed on biological productive land was three times greater than its carrying capacity.