Intersection channelization and signal timing are important for mitigating traffic congestion in the urban transportation system. Most existing studies fail to quantitively evaluate the severity of deadlock caused by the mismatch between lane allocation and signal timing, especially at a channelized intersection with auxiliary lanes. This study proposes a new indicator — average unavailable time ratio (AUTR)—to quantitively evaluate the impacts of such deadlock on traffic operational efficiency at a channelized intersection with an auxiliary lane, based on trajectory data. Deadlock states are coded at the vehicle movement level and the state transition is analyzed with varying signal timings. They are classified into four types based on the evolution of queue length with different signal timings using discharging shockwaves. AUTR is calculated by constructing a spatiotemporal diagram using trajectory data, and simulation studies validate the effectiveness of the proposed indicator. The AUTR value has a strong positive correlation with vehicle travel time and queueing time caused by the deadlock and measures the severity of the deadlock. The storage length of the auxiliary lane has a greater impact on AUTR than the bay taper length. The impacts of lane allocation on the deadlock are affected by signal timings. This proposed method can effectively evaluate the rationality of lane allocation designs with auxiliary lanes given a signal timing scheme.