Continuous-time score-based generative models consist of a pair of stochastic differential equations (SDEs)—a forward SDE that smoothly transitions data into a noise space and a reverse SDE that incrementally eliminates noise from a Gaussian prior distribution to generate data distribution samples—are intrinsically connected by the time-reversal theory on diffusion processes. In this paper, we investigate the use of stochastic evolution equations in Hilbert spaces, which expand the applicability of SDEs in two aspects: sample space and evolution operator, so they enable encompassing recent variations of diffusion models, such as generating functional data or replacing drift coefficients with image transformation. To this end, we derive a generalized time-reversal formula to build a bridge between probabilistic diffusion models and stochastic evolution equations and propose a score-based generative model called Hilbert Diffusion Model (HDM). Combining with Fourier neural operator, we verify the superiority of HDM for sampling functions from functional datasets with a power of kernel two-sample test of 4.2 on Quadratic, 0.2 on Melbourne, and 3.6 on Gridwatch, which outperforms existing diffusion models formulated in function spaces. Furthermore, the proposed method shows its strength in motion synthesis tasks by utilizing the Wiener process with values in Hilbert space. Finally, our empirical results on image datasets also validate a connection between HDM and diffusion models using heat dissipation, revealing the potential for exploring evolution operators and sample spaces.