Security is the main concern and bottleneck for widely deployed wireless applications due to the fact that wireless channels are vulnerable to attacks and that wireless bandwidth is a constrained resource. In this sense, it is desirable to adaptively achieve security according to the available resource. In particular, mobile ad hoc networks (MANETs) based on cooperative communication (CC) present significant challenges to security issues, as well as issues of network performance and management. In this paper, we focus on authentication and topology control issues. Although authentication and topology control are separately studied in most existing works, they are, in fact, closely correlated in MANETs. For example, both authentication and topology control schemes have significant impacts on throughput. In this paper, we jointly consider authentication and topology control. Specifically, we analyze the effective throughput with upper layer authentication schemes and physical-layer schemes related to channel conditions and relay selections for CCs. A joint authentication and topology control (JATC) scheme is proposed to improve the throughput. JATC is formulated as a discrete stochastic optimization problem, which does not require prior perfect channel status but only channel estimate. We also mathematically prove the tracking convergence property and the convergence rate of the discrete stochastic optimization approach in this paper. Simulation results show that our scheme can substantially improve throughput in MANETs with CC.