Multiple Clock Domain (MCD) processors are a promising future alternative to today's fully synchronous designs. Dynamic Voltage and Frequency Scaling (DVFS) in an MCD processor has the extra flexibility to adjust the voltage and frequency in each domain independently. Most existing DVFS approaches are profile-based offline schemes which are mainly suitable for applications whose execution characteristics are constrained and repeatable. While some work has been published about online DVFS schemes, the prior approaches are typically heuristic-based. In this paper, we present an effective online DVFS scheme for an MCD processor which takes a formal analytic approach, is driven by dynamic workloads, and is suitable for all applications. In our approach, we model an MCD processor as a queue-domain network and the online DVFS as a feedback control problem with issue queue occupancies as feedback signals. A dynamic stochastic queuing model is first proposed and linearized through an accurate linearization technique. A controller is then designed and verified by stability analysis. Finally we evaluate our DVFS scheme through a cycle-accurate simulation with a broad set of applications selected from MediaBench and SPEC2000 benchmark suites. Compared to the best-known prior approach, which is heuristic-based, the proposed online DVFS scheme is substantially more effective due to its automatic regulation ability. For example, we have achieved a 2-3 fold increase in efficiency in terms of energy-delay product improvement. In addition, our control theoretic technique is more resilient, requires less tuning effort, and has better scalability as compared to prior online DVFS schemes. We believe that the techniques and methodology described in this paper can be generalized for energy control in processors other than MCD, such as tiled stream processors.