The low-altitude intelligent network (LAIN) serves as a fundamental driving force for the intelligent development of the low-altitude economy and aerial traffic systems. However, current low-altitude communication technologies still face significant challenges, including limited coordination capability and insufficient transmission reliability, which severely hinder their ability to support services in complex and weak networks. To address the above challenges, this paper proposes an intelligent integrated communication architecture for LAIN, which is vertically divided into three layers: the integrated network layer, the resource adaptation layer, and the low-altitude service layer. It incorporates key technologies such as cross-network collaborative transmission, flexible multipath scheduling, enhanced coding redundancy, and covert channel authentication. By integrating technology and architectural innovation, the framework aims to enhance communication efficiency and reliability. Experimental results demonstrate that the effective transmission rate of the proposed scheme is at least 1 times higher than that of single-link transmission, the decoding success rate of network coding improves by an average of 11.05% compared to traditional methods, and the transmission accuracy of the covert channel has been improved by at least 10% compared with other algorithms.