Alzheimer's disease (AD) is an age-related neurodegenerative brain disorder characterized by aggregation of amyloid-β (Aβ) peptide, formation of neurofibrillary tangles, synaptic loss, and neuronal cell death; however, the characteristic pathological alterations taking place in the “second brain”-enteric nervous system is still largely undefined. In this study, we aimed to detect the pathological changes in the APP/PS1 mice ileum by a novel whole mount technique. The deposition of Aβ plaque and the overexpression of phosphorylated Tau (pTau) protein were observed in the myenteric neurons of APP/PS1 mice. Compared to the control mice, the proportions of neuronal nitric oxide synthase (nNOS) + and choline acetyltransferase (ChAT) + neurons in the myenteric plexus of APP/PS1 mice significantly decreased (p < 0.05). Moreover, whole mount preparations and paraffin sections both demonstrated that the number of CD68+ macrophages in the APP/PS1 mice ileum significantly increased (p < 0.05). But, there was no significant difference (p > 0.05) in the number of enteric HuC/D+ neurons and the density of Tuj1 between the APP/PS1 and wild type mice, which may be due to the compensatory function of enteric nervous system. These results suggest that the deposition of Aβ plaque and pTau might activate the enteric resident macrophages, further leading to the loss of myenteric nitrergic and cholinergic neurons in the enteric nervous system.