Accurate time synchronization is essential for Internet of Things (IoT) systems, where multiple distributed nodes must share a common time base for coordinated sensing and data fusion. However, conventional synchronization approaches suffer from nondeterministic transmission latency, limited precision, or restricted bidirectional functionality. This paper presents a protocol-independent wireless timer synchronization method that exploits radio timeslots to transmit precisely timestamped beacons in a proprietary radio mode. By decoupling synchronization from upper-layer packet retransmissions and leveraging hardware-timed radio events, the proposed approach significantly reduces scheduling uncertainty and achieves nanosecond-level synchronization accuracy. Comprehensive experiments evaluate the impacts of synchronization frequency, RSSI, BLE connection interval, and throughput on synchronization performance. The results demonstrate that an optimal synchronization frequency of 1000 Hz yields an approximately 20 ns delay in the absence of communication stack activity while maintaining sub-500 ns accuracy under most realistic BLE traffic conditions. Furthermore, larger connection intervals, lower application throughput, and higher RSSI consistently improve synchronization quality by reducing radio resource contention and packet loss. The proposed scheme provides a general and high-precision synchronization solution suitable for resource-constrained IoT systems.