Water used for production is the primary consumer of regional water. Water footprint reflects the actual water consumption of each product, which can reflect the intensity of water consumption of each production sector and the flow of water resources implied in the product trade. In this paper, the water footprint of each sector in Henan Province in 2017 was calculated using non-competitive input-output techniques. Furthermore, a dual-objective planning model that minimizes water resource export and maximizes labor compensation was established, based on which the export structure of the sector in the province was optimized. Research findings show that agriculture is the primary consuming sector of water resources from the direct water use perspective. In comparison, the food processing industry is the major consuming sector of water resources from the water footprint perspective. The difference in water resources consumed by sectors from the perspective of water footprint is smaller than that from the perspective of direct water use. Second, most water-intensive sectors have a relatively large water footprint of out-of-province use, which results in 52.75% of Henan Province's produced water being consumed outside the province. Third, the current export structure adjustment of sectors in Henan Province can achieve a Pareto improvement of water conservation and economic development. It is expected to save 14.65% of the province's export water resources and increase Henan Province's total exports by 170.61 billion (170.61 × 109) yuan and increase labor compensation by 39.76 billion yuan. This study can be used to optimize water allocation and improve sustainable water use in water-scarce regions.