The purpose of the research was to discuss the application values of deep learning algorithm-based computed tomography perfusion (CTP) imaging combined with head and neck computed tomography angiography (CTA) in the diagnosis of ultra-early acute ischemic stroke. Firstly, 88 patients with acute ischemic stroke were selected as the research objects and performed with cerebral CTP and CTA examinations. In order to improve the effect of image diagnosis, a new deconvolution network model AD-CNNnet based on deep learning was proposed and used in patient CTP image evaluation. The results showed that the peak signal-to-noise ratio (PSNR) and feature similarity (FSIM) of the AD-CNNnet method were significantly higher than those of traditional methods, while the normalized mean square error (NMSE) was significantly lower than that of traditional algorithms (
P
<
0.05
). 80 cases were positive by CTP-CTA, including 16 cases of hyperacute ischemic stroke and 64 cases of acute ischemic stroke. The diagnostic sensitivity was 93.66%, and the specificity was 96.18%. The cerebral blood flow (CBF), cerebral blood volume (CBV), and the mean transit time (MTT) in the infarcted area were significantly greater than those in the corresponding healthy side area, and the time to peak (TTP) was significantly less than that in the corresponding healthy side area (
P
<
0.05
). The cerebral perfusion parameters CBF, TTP, and MTT in the penumbra were significantly different from those in the infarct central area and the corresponding contralateral area, and TTP was the most sensitive (
P
<
0.05
). To sum up, deep learning algorithm-based CTP combined with CTA could find the location of cerebral infarction lesions as early as possible to provide a reliable diagnostic result for the diagnosis of ultra-early acute ischemic stroke.