A fundamental process of vision involves segmenting visual scenes into distinct objects and surfaces. Stereoscopic depth and visual motion are important cues for segmentation. However, the mechanisms by which the visual system utilizes depth and motion cues to segment multiple objects are not fully understood. We investigated how neurons in the middle-temporal (MT) cortex of macaque monkeys represented overlapping surfaces located at different depths and moved simultaneously in different directions. We recorded neuronal activities in the MT of three male monkeys while they performed discrimination tasks under different attention conditions. We found that neuronal responses to overlapping surfaces showed a robust bias toward the horizontal binocular disparity of one of the two surfaces. Across all animals, the disparity bias of a neuron in response to two surfaces positively correlated with the neuron's disparity preference for a single surface. For two animals, neurons that preferred near disparities of single surfaces (near neurons) showed a near bias to overlapping stimuli, whereas neurons that preferred far disparities (far neurons) showed a far bias. For the third animal, both near and far neurons displayed a near bias, although the near neurons showed a stronger near bias than the far neurons. Interestingly, for all three animals, both near and far neurons exhibited an initial near bias relative to the average of the responses to the individual surfaces. Although attention can modulate neuronal response to better represent the attended surface, the disparity bias was not due to attention. We also found that the effect of attention modulation on MT responses was consistent with object-based rather than feature-based attention. We proposed a model in which the pool size of the neuron population that weighs the responses to individual stimulus components can be variable. This model is a novel extension of the standard normalization model and provides a unified explanation for the disparity bias observed across animals. Our results revealed the neural encoding rule for multiple stimuli located at different depths and presented new evidence of response modulation by object-based attention in MT. The disparity bias allows subgroups of neurons to preferentially represent individual surfaces of multiple stimuli at different depths, thereby facilitating segmentation.