Fractional-order vortex beams (FO-VBs) exhibit complex phase structures, distinct from their integer-order counterparts, particularly featuring gap discontinuities and rich dynamics during propagation. However, high-resolution measurement of their actual phase evolution remains a challenge. This study introduces a compact, improved single-element heterodyne interferometer designed for precise, direct measurement of the wavefront phase of FO-VBs in free space. Our setup successfully captured the intricate phase distribution within the radial dark region, revealing that it comprises a series of vortex–antivortex pairs with opposite topological charges. Theoretical and experimental results demonstrate that as the fractional part of the topological charge increases, the phase fluctuation region from a single pair expands. Upon approaching an integer charge, these pairs annihilate head-to-tail, culminating in a complete 2π phase jump and the formation of a new primary vortex. Concurrently, beam quality degrades from integer to half-integer order, reaching its minimum at the latter, which aligns with the variation trend of the phase distribution, demonstrating an intrinsic link between beam quality and phase structure. This robust interferometric method, with the capability for phase distribution reconstruction even under obstructed conditions, provides critical insights into the phase dynamics of FO-VBs and is anticipated to be a valuable tool for predicting beam quality evolution and interaction effects in complex media, such as atmospheric turbulence.