In the Pulse Position Modulation (PPM) space optical communication channel estimation based on photon detection, two schemes for the estimation of signal photon average and background photon average are proposed. Scheme 1 is based on the characteristic of M-order PPM, where only one of the M slots has a signal optical slot. The signal photon average and the background photon average are roughly estimated by comparing the number of photons in each slot in each symbol counted by the photon detector and by counting the total number of photons in each slot in the error correction frame. The proposed method in scheme 2 is based on that in scheme 1. The signal optical slot position is re-determined by decision feedback in the Serially Concatenated Pulse Position Modulation (SCPPM) system. Since the existence of SCPPM accumulator leads to error propagation, the soft information output by decoding is first interleaved, and then mapped from bit to PPM symbols after hard decision and accumulation. Finally, the position of signal optical slot is re-determined to obtain more accurate signal photon average and background photon average.