Abstract: Scientifically measuring the synergy between agricultural product upgrading and rural E-commerce is of great significance for deeply promoting the conversion of new and old kinetic energy in the agricultural sector and advancing high-quality rural economic development. Taking the Shandong Pilot Zone for the Conversion of New and Old Kinetic Energy as the research object, this study employs a coupling coordination degree model and Markov chains to systematically analyze the characteristics and evolutionary trends of the coupling relationship between the two; Meanwhile, it uses the geodetector and geographically and temporally weighted regression (GTWR) model to explore the spatiotemporal heterogeneous impact of the driving factors on the coupling coordination degree. Results show that: 1) from 2017 to 2022, there was a significant polarization in the development of the two within the pilot zone; the synergy showed a “rise–decline–rise” trend in the temporal dimension and conformed to the regional development pattern of “one cluster, two cores, and three circles” in the spatial dimension; 2) the state of synergy was highly stable: the provincial capital economic circle and the Jiaodong economic circle were “active zones”, while the southern Shandong economic circle was a “depressed zone”; moreover, eight cities including Liaocheng and Dezhou faced the risk of “fatigued development” that might regress into severe disorder; 3) digital infrastructure was the dominant factor affecting the synergy, innovation input served as the core driving engine, while the high-end service industry exerted a negative impact, revealing a structural mismatch between its supply structure and the demand for agricultural digital transformation. Based on this, it is recommended to leverage the radiating and driving effects of Qingdao and Jinan, make up for the shortcomings of cities such as Liaocheng and Dezhou, and cultivate characteristic new kinetic energy in cities such as Dongying and Zaozhuang, so as to improve the coordinated development level of the two.