Recently, toehold-mediated DNA strand displacement reaction has been widely used in detecting molecular signals. However, traditional strand displacement, without cooperatively signaling among DNA inputs, is insufficient to design more complicated nanodevices. In this work, a logic computing system is established using the cooperative "binding-induced" mechanism, based on the AuNP-based beacons, in which five kinds of multiple-input logic gates have been constructed. This system can recognize DNA and protein streptavidin (SA) simultaneously. Finally, the manipulations of the logic system are also demonstrated by controlling programmed conjugate DNA/AuNP clusters. This study provides possibilities to detect multiple input signals and design complex nanodevices, and can be potentially applied to the detection of multiple molecular targets and construction of the large-scale DNA-based computation.