Despite growing studies on the distinction between morphological and functional polycentricity, the present methods for identifying polycentricity often focus on the morphological dimension due to a lack of information about intra-urban functional flows, and are limited by the multifarious nature of people’s spatiotemporal interactions. This study proposes a new approach, examining the degree of polycentricity in Shanghai at the intra-urban level using passive mobile phone data. A series of polycentricity indicators are used and are benchmarked against previous studies. Notably, we found that people’s daily movements within a subcenter indicate that morphological polycentricity is also at play in Shanghai. We conclude that morphological and functional polycentricity may coexist at the intra-urban level, and that a mobile phone data approach can offer an alternative method to elucidate both the morphological and functional features of subcenters.