Green production is the inevitable course to develop agriculture sustainably. To explore the effective methods of green production, the key area of modern agriculture, for family farms is of considerable theoretical value and practical significance. This study empirically analyzed the influence of family farms joining cooperatives on green production and its mechanism using the ranking selection and explanatory structure models based on the investigation data of 422 provincial demonstration family farms in Shandong Province. 1) Quantitative analysis showed that the proportion of green production of family farms joining cooperatives was evidently higher than that of farms not joining cooperatives. 2) From heterogeneity analysis, the proportion of green production by cooperative leaders’ farms was higher than that of farms with ordinary members. Joining cooperatives was significant for the green production of grain and vegetable family farms but not for fruit and livestock breeding farms. Joining the cooperative had a significant impact on the green production of medium-sized (10–20 people) farms but had no significant impact on the behavior of small-scale (less than 10 persons) and large-scale (more than 20 persons) farms. 3) After the family farm joined the cooperative, the three green production behaviors with the highest adoption rates were applying organic fertilizer (74.35%), water-saving irrigation (68.17%), and subsoiling (65.80%). In contrast, the three green production behaviors with the lowest adoption rates were ecological treatment of livestock and poultry breeding waste (26.84%), recycling pesticide waste (41.81%), and integration of water and fertilizer. 4) The regression equation results showed that family farms significantly increased the possibility of green production by joining cooperatives. Under the control of other variables, joining the cooperative had a significant positive impact on the green production of family farms at the 1% level, with an impact coefficient of 0.554, and the promotion of water-saving irrigation, application of organic fertilizer, and integration of water and fertilizer were more prominent. After considering other control variables, family farm management type, labor force, product quality certification, traceability of origin, and awareness and willingness toward green production all influenced green production. 5) From the explanatory structure model analysis, seven significant influencing factors played independent roles and were also interrelated, forming a complete chain of influencing factors for family farms to participate in green production. Joining the cooperative as a deep-rooted factor directly affected the origin traceability and product quality certification of family farm products and affected the green production of family farms from the source along the positive conduction relationship of “family farm green production cognition → green production willingness →green production behavior”. Therefore, we should encourage and support family farms to join cooperatives, focus on the heterogeneity between farms, and promote green production on farms through the training and supervision of cooperatives.