Quantum computers can solve problems that are inefficiently solved by classical computers, such as integer factorization. A fully programmable quantum computer requires a quantum control microarchitecture that connects the quantum software and hardware. Previous research has proposed a Quantum Instruction Set Architecture (QISA) and a quantum control microarchitecture, which targets Noisy Intermediate-Scale Quantum (NISQ) devices without fault-tolerance. However, fault-tolerant (FT) quantum computing requires FT implementation of logical operations, and repeated quantum error correction, possibly at runtime. Though highly patterned, the amount of required (physical) operations to perform logical operations is ample, which cannot be well executed by existing quantum control microarchitectures. In this paper, we propose a control microarchitecture that can efficiently support fault-tolerant quantum computing based on the rotated planar surface code with logical operations implemented by lattice surgery. It highlights a two-level address mechanism which enables a clean compilation model for a large number of qubits, and microarchitectural support for quantum error correction at runtime, which can significantly reduce the quantum program codesize and present better scalability.