This paper reports a pulse inversion chirp coded tissue harmonic imaging (PI-CTHI) method for visualizing small animal hearts that provides fine spatial resolution at a high frame rate without sacrificing the echo signal to noise ratio (eSNR). A 40 MHz lithium niobate (LiNbO(3)) single element transducer is employed to evaluate the performance of PI-CTHI by scanning tungsten wire targets, spherical anechoic voids, and zebrafish hearts. The wire phantom results show that PI-CTHI improves the eSNR by 4 dB from that of conventional pulse inversion tissue harmonic imaging (PI-THI), while still maintaining a spatial resolution of 88 and 110 μm in the axial and lateral directions, respectively. The range side lobe level of PI-CTHI is 11 dB lower than that of band-pass filtered CTHI (or F-CTHI). In the anechoic sphere phantom study, the contrast-to-noise ratio of PI-CTHI is found to be 2.7, indicating a 34% enhancement over conventional PI-THI. Due to such improved eSNR and contrast resolution, blood clots in zebrafish hearts can be readily visualized throughout heart regeneration after 20% of the ventricle is removed. Disappearance of the clots in the early stages of the regeneration has been observed for 7 days without sacrificing the fish.