We present enhanced truncated-correlation phototothermal coherence tomography (eTC-PCT) for non-invasive three-dimensional imaging of small animals. Tumor detection is reported in a mouse thigh by injecting cancerous cells in the thigh followed by eTC-PCT imaging. Detection of the tumor 3 days after injection may lead to potential for using the eTC-PCT method for cancer treatment studies. eTC-PCT was also applied successfully to non-invasive in-vivo mouse brain structural imaging. A unique spatial-gradient-gate adaptive filter was introduced in a scanned mode along the (x,y) coordinates of camera images from different sub-cranial depths, revealing absorber true spatial extent from diffusive photothermal images and restoring pre-diffusion lateral image resolution beyond the Rayleigh criterion limit in diffusion-wave imaging science. The spatial resolution and contrast enhancement demonstrated in photothermal in-vivo and ex-vivo images of the mouse brain revealed not only vascular structures but also other brain structures, such as the brain hemispheres, cerebellum, and olfactory lobes.