The paigeite resources are abundant in China, but most of them are difficult to be utilized efficiently because of the current technical problems on industrial practice. It is necessary to perfected and innovated for comprehensive utilization of paigeite. The new process of gas-based shaft furnace direct reduction-electric furnace smelting separation provides a new way to efficient and clean comprehensive utilization of paigeite resources. In this paper, the pellets are prepared from boron-bearing iron concentrate. The mechanisms of roasting, the rules of reduction, and the properties of reduction swelling are also investigated. And then the pellets after reduction are smelted and separated in electric furnace to study the properties of products and analyze the feasibility and superiority of new technique. The results showed that boron-bearing iron concentrate is a kind of good raw material for pelletizing process. The properties of boron-bearing pellets after roasting for 20 min at 1200°C could meet to the requirements of gas-based shaft furnace direct reduction process, which exhibited fast reaction rate, good reduction swelling properties and high compressive strength both before and after reduction. With the new process, the efficient separation of boron and iron can be realized. The high boron grade and high activity of boron-rich slag obtained from new process can be used directly in boric acid manufacture. The new process shows excellent tech-economy feasibility to achieve efficiency and clean comprehensive utilization of paigeite resources.