LiDAR (Light Detection and Ranging) imaging based on SPAD (Single-Photon Avalanche Diode) technology suffers from severe area penalty for large on-chip histogram peak detection circuits required by the high precision of measured depth values. In this work, a probabilistic estimation-based super-resolution neural network for SPAD imaging that firstly uses temporal multi-scale histograms as inputs is proposed. To reduce the area and cost of on-chip histogram computation, only part of the histogram hardware for calculating the reflected photons is implemented on a chip. On account of the distribution rule of returned photons, a probabilistic encoder as a part of the network is first proposed to solve the depth estimation problem of SPADs. By jointly using this neural network with a super-resolution network, 16× up-sampling depth estimation is realized using 32 × 32 multi-scale histogram outputs. Finally, the effectiveness of this neural network was verified in the laboratory with a 32 × 32 SPAD sensor system.