Shared secret-key extraction from random channel characteristics is an effective approach to ensuring the physical layer security of atmospheric optical channels. The secret-key generation rate and disagreement rate are two issues that attract a lot of attention. Using the random characteristics of atmospheric turbulent optical channels as a shared source of randomness, a secret-key extraction scheme for multiple-input multiple-output (MIMO) atmospheric optical channels is proposed. The alternative singular value decomposition is used to decompose the channel matrix; the correlation between the two channel characteristic sequences obtained by the two legitimate parties is enhanced through a simple moving average, and the single-threshold interleaved quantization is performed on the channel characteristic sequences after moving average. The two legitimate parties generate random controlling sequences for coding mapping based on differential diversity values, in order to implement encoding mapping for the single threshold interleaved quantization results of the channel characteristic sequences. The experimental results show that our scheme’s initial key disagreement rate can reach 4.5×10^-5 at a signal-to-noise ratio of 30 dB, and that the generated random bit sequences have passed the National Institute of Standards and Technology (NIST) randomness test. The results are useful in the implementation of secret-key extraction from atmospheric MIMO optical channels.