The integration of financial technology expenditures and green total factor productivity (GTFP) constitutes a critical impetus for sustainable economic advancement. This study employs provincial panel data from China (2012–2020) and uses the SBM model with undesirable outputs, the PVAR model, moderation effect analysis, and threshold regression to investigate the underlying mechanisms and threshold effects of financial technology expenditure on GTFP. The results show that (1) financial technology expenditure has a significant promoting effect on the growth of GTFP, with a coefficient of 0.614 (p < 0.05), indicating the need for further increases in fiscal investment in science and technology; (2) the effect of financial technology expenditure on GTFP varies across the eastern, central, and western regions of China, with stronger effects observed in the eastern region, suggesting that the government should formulate differentiated financial technology expenditure policies on the basis of local conditions; and (3) that educational investment and industrial upgrading play strong moderating roles in the impact of financial technology expenditure on GTFP, with interaction term coefficients of 0.059 (p < 0.05) and 0.206 (p < 0.1), respectively. Threshold analysis further reveals that the positive effect strengthens significantly once educational investment surpasses a log value of 9.3674 and industrial upgrading exceeds a ratio of 0.0814. However, currently, China’s education investment and industrial structure upgrading are still insufficient, necessitating further increases in education investment and promoting the transformation and upgrading of the industrial structure.