Growing reports indicate that Sprouty (SPRY) isoforms act as inhibitors or promoters in various types of cancers. And the occurrence of different cancers may be related to the abnormal expression of one of the SPRY isoforms. The identification of SPRY isoforms thus plays a particularly important role in determining which isoform's aberrant expression inhibits or promotes cancer. But their own properties, such as similarities in the structure and molecular weight, make their identification particularly difficult. In this article, we propose a novel method to identify SPRY isoforms using atomic force microscopy (AFM) by observing differential binding of different SPRY isoforms to bovine serum albumin (BSA), which can be used to distinguish SPRY isoforms at the single-molecule level. Specific binding of SPRY1 and BSA was observed by AFM. The reduction in the number of monomeric protein molecules caused by the partial depletion of these two proteins during binding is also consistent with the weakening of the monomeric protein bands in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). At the same time, the arrangement of the two proteins in a tightly bound complex was also observed. However, the SPRY3 isoform did not interact with BSA to cause aggregation, and the diameter and height of the two proteins did not change significantly compared to those before the reaction. In this way, with the participation of BSA, the two isoforms, SPRY1 and SPRY3, can be identified and separated using atomic force microscopy. In addition, the experimental result that the formation of the SPRY1–BSA complex can selectively reduce the concentration of SPRY1 isoforms in the environment will also contribute to future research on anticancer drugs influenced by SPRY1.