Nowadays, the intelligent unmanned agricultural unmanned aerial vehicle (UAV) swarm collaboration network (AUSCN) has fully demonstrated its advantages in agricultural monitoring and management. By using an AUSCN, multi-machine cooperation can be realized to expand the detection range, and more complex tasks can be completed without human participation, so as to improve work efficiency and reduce the consumption of manpower and material resources. In AUSCNs, clustering is a key method to lower energy consumption. However, there is a challenge to select cluster heads in AUSCNs because of the limitation of transmission distances and the complexity of network topological structures. In addition, this problem has been confirmed as NP-hard. In this paper, a new niche adaptive elite evolutionary algorithm (NAEEA) is proposed to solve this problem. NAEEAs can search within various complicated stochastic situations at high speeds with characterized high precision and fast convergence. This algorithm integrates the merits of elite selection and adaptive adjusting to achieve high performance. In NAEEAs, a new adaptive operator is designed to speed up the convergence rate, while a novel elite operator is proposed to avoid local optima and raise the exploration ability. Furthermore, a new niche operator is also proposed to increase the population diversity. The simulation results show that, compared with an evolutionary algorithm (EA), a simulated annealing algorithm (SA) and a leapfrog algorithm (SFLA), clustering energy consumption based on an NAEEA is significantly reduced, and the network energy consumption of the AUSCN is up to 21.43%, 25.00% and 25.76% lower than the other three algorithms, respectively.