The shifting of plant flowering phenology is a climate change fingerprint found in natural systems around the world, especially in cases of increasing temperatures and related environmental changes. It is critical to understand the impact of flowering phenological shifts on plant-pollinator communities, in order to predict fluctuations in ecosystem service and community structure under the effects of climate change. Despite the possibility that a phenological shift in one plant species may affect other plants via shared pollinators (e.g., indirect plant-plant interactions, including apparent facilitation or competition), few studies have experimentally manipulated flowering times to examine the consequences and underlying mechanisms of such shifts on plant reproductive success. This is particularly true for subtropical communities, in which shifts in the flowering times of a short flowering plant may influence the pollinator visits and seed sets of a year-round flowering plant, due to new overlapping times of flowering that did not previously exist. Here, we studied how flowering phenology shifts in the short flowering, native Eupatorium formosanum affected pollinator visits and seed sets, as well as in the neighboring, year-round flowering, non-native Bidens pilosa var. radiata. Our study included a flowering time treatment (advanced [July–August], current [September–October], and delayed [November–December] flowering in E. formosanum) and a neighbor plant treatment (field plots with B. pilosa alone, B. pilosa + E. formosanum, and E. formosanum alone). We observed and recorded the pollinator visits and seed sets to both plant species almost weekly in a subtropical national park in Taipei, Taiwan. The results showed the following: 1) The flowering time and neighbor plant treatments influenced the reproductive success of B. pilosa, but these two treatment effects did not interact, suggesting that though phenological shifts may not change the direction (apparent competition) and magnitude (competition hierarchy) of the indirect plant-plant interaction between the two plant species, each of these two effects did influence the reproductive success of B. pilosa. Specifically, not only was there a decrease in pollinator visits to B. pilosa over time (delayed time period), E. formosanum’s presence reduced both the pollinator visits and seed sets of B. pilosa. This indicated apparent competition between the two plant species, in which B. pilosa was negatively affected by E. formosanum, but E. formosanum was not affected. 2) Though B. pilosa and E. formosanum shared pollinators, insect visitor communities differed across flowering time and neighbor plant treatments. For B. pilosa, insect visitors decreased in abundance and richness over time and when in the presence of E. formosanum. Pollinator compositions also changed across treatments, most notable of which more efficient pollinators preferred E. formosanum in the B. pilosa + E. formosanum treatment group. 3) Plant-pollinator interaction network structures differed (weighted connectance, interaction evenness, and vulnerability) across neighbor plant treatment groups, suggesting that communities with both B. pilosa and E. formosanum altered plant-pollinator interactions. Overall, our results suggest that phenological shifts in a short flowering plant can impact the reproductive success of a year-round flowering plant, likely due to competition for more efficient pollinators and changes in pollinator compositions, ultimately altering plant-pollinator interaction network structures. We recommend that conservation management plans consider how different flowering times and neighbor plants affect indirect plant-plant interactions, potentially reshaping local plant-pollinator communities in the face of climate change.