We report a frequency-multiplexing method for multi-beam photon-counting light detection and ranging (LiDAR), where only one single-pixel single-photon detector is employed to simultaneously detect the multi-beam echoes. In this frequency-multiplexing multi-beam LiDAR, each beam is from an independent laser source with different repetition rates and independent phases. As a result, the photon counts from different beams could be discriminated from each other due to the strong correlation between the laser pulses and their respective echo photons. A 16-beam LiDAR system was demonstrated in three-dimensional laser imaging with 16 pulsed laser diodes at 850 nm and one single-photon detector based on a Si-avalanche photodiode. This frequency-multiplexing method can greatly reduce the number of single-photon detectors in multi-beam LiDAR systems, which may be useful for low-cost and eye-safe LiDAR applications.